Interaction between DNA ligase 3 (3l2p_A) and Nucleic acid (3l2p_D_B_C)

PDB and SCOP data

PDB ID: 3l2p (all binary interactions in this PDB entry)

Title: Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching Between Two DNA Bound States

Release date: 2010-07-14

Resolution: 3.0 Å

  • Chain A: 3l2p_A

    Title: DNA ligase 3

    Source organism: Homo sapiens

    Number of residues: 579 (44 missing in structure)

  • Chain B: 3l2p_D_B_C

    Title: Nucleic acid

    Number of residues: 42

    Note: Residues of nucleic acid domain are renumbered to avoid repeating the same residue numbers from different PDB chains.

Buried interface area: 2254.61 Å2

Number of inter-residue contacts at the interface: 175

Number of H-bonds: 31

  • Pairwise interaction

    Download PDB coordinates

    Download PyMOL visualization script

  • Biological assembly

    Homomer, 1 protein, 1 nucleic acid.

    Download PDB coordinates


Create a structural model for this interaction

  • Interface residues in 3l2p_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 190 23 P 26.4 23.5 %
    2 191 24 S 23.8 44.0 %
    3 192 25 Y 92.4 83.2 %
    4 193 26 N 49.9 41.4 %
    5 229 62 K 6.5 5.5 %
    6 231 64 V 42.7 46.2 %
    7 232 65 Y 3.6 26.1 %
    8 233 66 N 42.5 42.5 %
    9 234 67 L 16.2 83.3 %
    10 235 68 N 38.9 46.0 %
    11 236 69 D 0.5 3.5 %
    12 237 70 K 36.2 49.7 %
    13 238 71 Q 37.2 67.2 %
    14 241 74 K 19.8 23.9 %
    15 245 78 R 12.7 10.5 %
    16 301 134 T 39.0 44.5 %
    17 302 135 K 44.9 32.9 %
    18 303 136 E 49.3 79.4 %
    19 304 137 D 3.3 2.6 %
    20 331 164 H 7.9 15.4 %
    21 332 165 D 27.8 43.6 %
    22 334 167 K 15.4 19.6 %
    23 335 168 M 3.4 49.3 %
    24 336 169 N 46.1 42.4 %
    25 337 170 S 8.5 45.6 %
    26 338 171 G 27.9 68.9 %
    27 339 172 A 6.1 31.9 %
    28 340 173 K 36.0 33.7 %
    29 341 174 H 23.8 65.1 %
    30 351 184 Y 27.3 42.1 %
    31 355 188 K 5.6 33.9 %
    32 398 231 L 4.3 19.9 %
    33 399 232 A 5.0 93.1 %
    34 400 233 E 0.2 0.6 %
    35 401 234 A 2.2 6.2 %
    36 407 240 Y 5.4 8.9 %
    37 411 244 K 29.9 30.0 %
    38 423 256 D 7.4 21.5 %
    39 424 257 G 12.8 91.9 %
    40 425 258 E 40.8 77.6 %
    41 426 259 R 13.4 74.9 %
    42 440 273 S 21.6 87.2 %
    43 441 274 R 60.4 53.6 %
    44 442 275 S 16.1 24.9 %
    45 444 277 K 51.2 53.4 %
    46 445 278 P 3.6 3.2 %
    47 446 279 V 0.2 1.5 %
    48 447 280 L 15.6 14.4 %
    49 450 283 K 3.8 23.4 %
    50 473 306 E 2.5 51.5 %
    51 487 320 F 46.1 56.9 %
    52 488 321 G 27.5 52.4 %
    53 491 324 G 19.7 59.7 %
    54 492 325 V 30.1 36.7 %
    55 493 326 H 47.5 30.1 %
    56 494 327 K 55.6 42.7 %
    57 582 415 G 1.2 6.2 %
    58 583 416 K 38.3 44.2 %
    59 584 417 R 28.6 22.3 %
    60 585 418 H 24.4 24.1 %
    61 588 421 K 26.5 88.6 %
    62 590 423 K 11.1 49.1 %
    63 592 425 D 1.0 5.8 %
    64 593 426 Y 26.8 50.5 %
    65 613 446 G 9.1 91.7 %
    66 614 447 Q 33.9 29.9 %
    67 615 448 G 7.1 25.3 %
    68 616 449 S 34.2 29.4 %
    69 617 450 K 32.3 39.1 %
    70 622 455 S 14.7 65.4 %
    71 623 456 I 38.0 72.2 %
    72 640 473 T 13.3 100.0 %
    73 641 474 K 53.7 56.0 %
    74 642 475 C 5.7 96.8 %
    75 643 476 A 28.8 63.4 %
    76 644 477 G 14.3 36.6 %
    77 645 478 G 36.1 68.8 %
    78 646 479 H 13.0 39.9 %
    79 647 480 D 30.6 36.6 %
    80 648 481 D 33.6 35.4 %
    81 649 482 A 1.7 1.9 %
    82 703 536 S 25.5 54.0 %
    83 704 537 K 15.0 23.4 %
    84 705 538 S 40.7 65.2 %
    85 707 540 A 8.4 9.5 %
    86 708 541 H 22.9 49.4 %
    87 712 545 G 1.2 14.3 %
    88 713 546 I <0.1 0.6 %
    89 714 547 S 25.4 96.1 %
    90 715 548 I 11.8 50.8 %
    91 716 549 R 22.8 45.5 %
    92 717 550 F 89.5 95.7 %
    93 718 551 P 33.8 78.9 %
    94 719 552 R 55.3 86.1 %
    95 720 553 C 0.1 2.2 %

  • Interface residues in 3l2p_D_B_C

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 4 26:D1 A 0.5 0.3 %
    2 5 27:D1 G 38.3 22.2 %
    3 6 28:D1 T 62.1 33.6 %
    4 7 29:D1 C 87.4 55.9 %
    5 8 30:D1 C 92.5 60.4 %
    6 9 31:D1 G 73.9 42.8 %
    7 10 32:D1 A 87.2 54.1 %
    8 11 33:D1 C 93.9 52.8 %
    9 12 34:D1 G 114.5 63.7 %
    10 13 35:D1 A 98.6 65.6 %
    11 14 36:D1 C 89.1 56.5 %
    12 15 37:D1 G 89.2 49.5 %
    13 16 38:D1 C 75.9 46.0 %
    14 17 39:D1 A 31.4 19.3 %
    15 18 40:D1 T 3.0 1.5 %
    16 19 41:D1 C 66.1 38.5 %
    17 20 42:D1 C 58.1 42.0 %
    18 21 43:D1 C 25.3 14.8 %
    19 27 5:B1 A 2.0 1.3 %
    20 28 6:B1 T 58.6 28.8 %
    21 29 7:B1 G 89.0 55.4 %
    22 30 8:B1 C 73.3 44.7 %
    23 31 9:B1 G 73.5 41.0 %
    24 32 10:B1 T 113.7 67.4 %
    25 33 11:B1 C 120.1 80.7 %
    26 34 12:C1 G 106.5 69.0 %
    27 35 13:C1 T 99.1 67.4 %
    28 36 14:C1 C 68.7 41.4 %
    29 37 15:C1 G 52.6 28.4 %
    30 38 16:C1 G 50.1 30.2 %
    31 39 17:C1 A 12.8 6.9 %
    32 40 18:C1 C 69.4 44.0 %
    33 41 19:C1 T 58.9 37.0 %
    34 42 20:C1 G 19.5 6.1 %

No. Residue no. in chain A structure Residue no. in chain A sequence Residue in chain A Residue no. in chain B structure Residue no. of chain B in PDB Residue in chain B Contact area, Å2 Contact type
1 190 23 P 40 18:C1 C 26.4
2 191 24 S 40 18:C1 C 7.9
3 191 24 S 41 19:C1 T 15.9 H-bond
4 192 25 Y 7 29:D1 C 11.8
5 192 25 Y 8 30:D1 C 17.6
6 192 25 Y 38 16:C1 G 2.7
7 192 25 Y 39 17:C1 A 12.8
8 192 25 Y 40 18:C1 C 35.1 H-bond
9 192 25 Y 41 19:C1 T 12.4
10 193 26 N 41 19:C1 T 30.4 H-bond
11 193 26 N 42 20:C1 G 19.5 H-bond
12 229 62 K 31 9:B1 G 6.5
13 231 64 V 30 8:B1 C 23.5
14 231 64 V 31 9:B1 G 19.2
15 232 65 Y 30 8:B1 C 3.6
16 233 66 N 29 7:B1 G 22.7
17 233 66 N 30 8:B1 C 19.8 H-bond
18 234 67 L 29 7:B1 G 6.1
19 234 67 L 30 8:B1 C 10.2
20 235 68 N 29 7:B1 G 30.6 H-bond
21 235 68 N 30 8:B1 C 8.3
22 236 69 D 29 7:B1 G 0.5
23 237 70 K 28 6:B1 T 21.6
24 237 70 K 29 7:B1 G 14.5
25 238 71 Q 28 6:B1 T 22.5
26 238 71 Q 29 7:B1 G 14.7 H-bond
27 241 74 K 20 42:D1 C 1.0
28 241 74 K 21 43:D1 C 2.4
29 241 74 K 27 5:B1 A 2.0
30 241 74 K 28 6:B1 T 14.4
31 245 78 R 21 43:D1 C 12.7
32 301 134 T 18 40:D1 T 3.0
33 301 134 T 19 41:D1 C 36.0 H-bond
34 302 135 K 19 41:D1 C 27.0
35 302 135 K 20 42:D1 C 17.8
36 303 136 E 19 41:D1 C 3.1
37 303 136 E 20 42:D1 C 35.9 H-bond
38 303 136 E 21 43:D1 C 10.3
39 304 137 D 20 42:D1 C 3.3
40 331 164 H 30 8:B1 C 7.9
41 332 165 D 9 31:D1 G 20.8
42 332 165 D 10 32:D1 A 7.0
43 334 167 K 9 31:D1 G 5.9
44 334 167 K 10 32:D1 A 9.6
45 335 168 M 9 31:D1 G 3.4
46 336 169 N 8 30:D1 C 20.3
47 336 169 N 9 31:D1 G 25.8 H-bond
48 337 170 S 8 30:D1 C 4.3
49 337 170 S 9 31:D1 G 4.2
50 338 171 G 8 30:D1 C 23.9 H-bond
51 338 171 G 9 31:D1 G 4.1
52 339 172 A 8 30:D1 C 6.1
53 340 173 K 6 28:D1 T 5.3
54 340 173 K 7 29:D1 C 22.5
55 340 173 K 8 30:D1 C 8.2
56 341 174 H 7 29:D1 C 11.3
57 341 174 H 8 30:D1 C 12.2 H-bond
58 341 174 H 41 19:C1 T 0.3
59 351 184 Y 7 29:D1 C 27.3 H-bond
60 355 188 K 7 29:D1 C 5.6
61 398 231 L 34 12:C1 G 4.3
62 399 232 A 34 12:C1 G 5.0
63 400 233 E 5 27:D1 G 0.2
64 401 234 A 35 13:C1 T 2.2
65 407 240 Y 5 27:D1 G 5.4
66 411 244 K 4 26:D1 A 0.5
67 411 244 K 5 27:D1 G 29.4
68 423 256 D 33 11:B1 C 7.4
69 424 257 G 33 11:B1 C 12.8
70 425 258 E 32 10:B1 T 30.6
71 425 258 E 33 11:B1 C 10.2
72 426 259 R 33 11:B1 C 13.4
73 440 273 S 32 10:B1 T 20.6 H-bond
74 440 273 S 33 11:B1 C 1.0
75 441 274 R 32 10:B1 T 1.8
76 441 274 R 33 11:B1 C 25.7
77 441 274 R 34 12:C1 G 32.9 H-bond
78 442 275 S 32 10:B1 T 16.1 H-bond
79 444 277 K 31 9:B1 G 37.7
80 444 277 K 32 10:B1 T 13.5
81 445 278 P 32 10:B1 T 3.6
82 446 279 V 32 10:B1 T 0.2
83 447 280 L 31 9:B1 G 10.1
84 447 280 L 32 10:B1 T 5.4
85 450 283 K 32 10:B1 T 3.8
86 473 306 E 33 11:B1 C 2.5
87 487 320 F 13 35:D1 A 6.6
88 487 320 F 14 36:D1 C 1.2
89 487 320 F 32 10:B1 T 18.2
90 487 320 F 33 11:B1 C 20.0
91 488 321 G 14 36:D1 C 3.0
92 488 321 G 15 37:D1 G 24.5
93 491 324 G 15 37:D1 G 7.7
94 491 324 G 16 38:D1 C 12.0
95 492 325 V 16 38:D1 C 17.1
96 492 325 V 17 39:D1 A 13.0
97 493 326 H 16 38:D1 C 29.1 H-bond
98 493 326 H 17 39:D1 A 18.4
99 494 327 K 15 37:D1 G 37.8
100 494 327 K 16 38:D1 C 17.8 H-bond
101 582 415 G 7 29:D1 C 1.2
102 583 416 K 6 28:D1 T 30.7 H-bond
103 583 416 K 7 29:D1 C 7.6
104 584 417 R 6 28:D1 T 4.9
105 584 417 R 34 12:C1 G 17.4
106 584 417 R 35 13:C1 T 6.3
107 585 418 H 5 27:D1 G 3.2
108 585 418 H 6 28:D1 T 21.2
109 588 421 K 34 12:C1 G 15.4 H-bond
110 588 421 K 35 13:C1 T 11.1
111 590 423 K 34 12:C1 G 2.4
112 590 423 K 35 13:C1 T 8.7
113 592 425 D 35 13:C1 T 1.0
114 593 426 Y 35 13:C1 T 18.1 H-bond
115 593 426 Y 36 14:C1 C 8.7
116 613 446 G 11 33:D1 C 9.1
117 614 447 Q 10 32:D1 A 14.4
118 614 447 Q 11 33:D1 C 19.5 H-bond
119 615 448 G 10 32:D1 A 7.1
120 616 449 S 9 31:D1 G 9.6 H-bond
121 616 449 S 10 32:D1 A 24.5 H-bond
122 617 450 K 10 32:D1 A 23.9
123 617 450 K 11 33:D1 C 8.3
124 617 450 K 38 16:C1 G <0.1
125 622 455 S 10 32:D1 A 0.7
126 622 455 S 11 33:D1 C 14.0 H-bond
127 623 456 I 11 33:D1 C 22.1
128 623 456 I 12 34:D1 G 15.9
129 640 473 T 12 34:D1 G 1.8
130 640 473 T 13 35:D1 A 11.5 H-bond
131 641 474 K 12 34:D1 G 32.3 H-bond
132 641 474 K 13 35:D1 A 21.3 H-bond
133 642 475 C 12 34:D1 G 5.7
134 643 476 A 11 33:D1 C 20.9
135 643 476 A 12 34:D1 G 7.9
136 644 477 G 11 33:D1 C <0.1
137 644 477 G 35 13:C1 T 1.2
138 644 477 G 36 14:C1 C 13.0
139 644 477 G 37 15:C1 G <0.1
140 645 478 G 36 14:C1 C 15.2
141 645 478 G 37 15:C1 G 20.9
142 646 479 H 37 15:C1 G 13.0
143 647 480 D 37 15:C1 G 15.2
144 647 480 D 38 16:C1 G 15.5
145 648 481 D 37 15:C1 G 3.4
146 648 481 D 38 16:C1 G 30.2 H-bond
147 649 482 A 38 16:C1 G 1.7
148 703 536 S 13 35:D1 A 7.2 H-bond
149 703 536 S 14 36:D1 C 18.3 H-bond
150 704 537 K 14 36:D1 C 10.4
151 704 537 K 15 37:D1 G 4.6
152 705 538 S 14 36:D1 C 26.2
153 705 538 S 15 37:D1 G 14.5
154 707 540 A 14 36:D1 C 8.4
155 708 541 H 13 35:D1 A 15.0
156 708 541 H 14 36:D1 C 7.9
157 712 545 G 14 36:D1 C 1.2
158 713 546 I 14 36:D1 C <0.1
159 714 547 S 13 35:D1 A 13.0
160 714 547 S 14 36:D1 C 12.4
161 715 548 I 13 35:D1 A 11.8
162 716 549 R 12 34:D1 G 3.0
163 716 549 R 13 35:D1 A 5.6
164 716 549 R 33 11:B1 C 14.2
165 717 550 F 12 34:D1 G 22.6
166 717 550 F 13 35:D1 A 0.9
167 717 550 F 33 11:B1 C 12.9
168 717 550 F 34 12:C1 G 29.2
169 717 550 F 35 13:C1 T 23.8
170 718 551 P 12 34:D1 G 25.2
171 718 551 P 13 35:D1 A 5.6
172 718 551 P 35 13:C1 T 3.0
173 719 552 R 35 13:C1 T 23.7
174 719 552 R 36 14:C1 C 31.6
175 720 553 C 36 14:C1 C 0.1

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A3l2p_A901AMP 284.555.9

  • Query protein: sp|P49916|DNLI3_HUMAN DNA ligase 3 OS=Homo sapiens GN=LIG3 PE=1 SV=2

    Result domain: 3l2p_A; DNA ligase 3

    Alignment data:

    Expectation value = 0, Score = 1207 bits (3122),

    Identities = 100% (577/577), Positive = 100% (577/577), Gaps = 0% (0/577).

    Interface alignment data:

    Interface residues in alignment: 100% (95/95).

    Identities = 100% (95/95), Positive = 100% (95/95), Gaps = 0% (0/95).

    Query: 257 RHKDCLLREFRKLCAMVADNPSYNTKTQIIQDFLRKGSAGDGFHGDVYLTVKLLLPGVIK 316

    RHKDCLLREFRKLCAMVADNPSYNTKTQIIQDFLRKGSAGDGFHGDVYLTVKLLLPGVIK

    3l2p_A: 3 RHKDCLLREFRKLCAMVADNPSYNTKTQIIQDFLRKGSAGDGFHGDVYLTVKLLLPGVIK 62

    dssp: --HHHEHHHHHHHHHHHH----HHHHHHHHHHHHH-- --HHHHHHHH------


    Query: 317 TVYNLNDKQIVKLFSRIFNCNPDDMARDLEQGDVSETIRVFFEQSKSFPPAAKSLLTIQE 376

    TVYNLNDKQIVKLFSRIFNCNPDDMARDLEQGDVSETIRVFFEQSKSFPPAAKSLLTIQE

    3l2p_A: 63 TVYNLNDKQIVKLFSRIFNCNPDDMARDLEQGDVSETIRVFFEQSKSFPPAAKSLLTIQE 122

    dssp: ------HHHHHHHHHHHH---HHHHHHHHHH--HHHHHHHHHH-------------EHHH


    Query: 377 VDEFLLRLSKLTKEDEQQQALQDIASRCTANDLKCIIRLIKHDLKMNSGAKHVLDALDPN 436

    VDEFLLRLSKLTKEDEQQQALQDIASRCTANDLKCIIRLIKHDLKMNSGAKHVLDALDPN

    3l2p_A: 123 VDEFLLRLSKLTKEDEQQQALQDIASRCTANDLKCIIRLIKHDLKMNSGAKHVLDALDPN 182

    dssp: HHHHHHHHH----HHHHHHHHHHHH-----HHHHHHHHHH---------HHHHHH-----


    Query: 437 AYEAFKASRNLQDVVERVLHNAQEVEKEPGQRRALSVQASLMTPVQPMLAEACKSVEYAM 496

    AYEAFKASRNLQDVVERVLHNAQEVEKEPGQRRALSVQASLMTPVQPMLAEACKSVEYAM

    3l2p_A: 183 AYEAFKASRNLQDVVERVLHNAQEVEKEPGQRRALSVQASLMTPVQPMLAEACKSVEYAM 242

    dssp: HHHHHHH---HHHHHHHHHHHHH--- --------------EEEE---HHHHH


    Query: 497 KKCPNGMFSEIKYDGERVQVHKNGDHFSYFSRSLKPVLPHKVAHFKDYIPQAFPGGHSMI 556

    KKCPNGMFSEIKYDGERVQVHKNGDHFSYFSRSLKPVLPHKVAHFKDYIPQAFPGGHSMI

    3l2p_A: 243 KKCPNGMFSEIKYDGERVQVHKNGDHFSYFSRSLKPVLPHKVAHFKDYIPQAFPGGHSMI 302

    dssp: HH----EEEEE----EEEEEEEE--EEEEE-----E--HHH---HHH-HHHH-----EEE


    Query: 557 LDSEVLLIDNKTGKPLPFGTLGVHKKAAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKF 616

    LDSEVLLIDNKTGKPLPFGTLGVHKKAAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKF

    3l2p_A: 303 LDSEVLLIDNKTGKPLPFGTLGVHKKAAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKF 362

    dssp: EEEEEEEE------E--HHHH-HHHHHH-----EEEEEEEEEEE--EE-----HHHHHHH


    Query: 617 LHDNMVEIPNRIMFSEMKRVTKALDLADMITRVIQEGLEGLVLKDVKGTYEPGKRHWLKV 676

    LHDNMVEIPNRIMFSEMKRVTKALDLADMITRVIQEGLEGLVLKDVKGTYEPGKRHWLKV

    3l2p_A: 363 LHDNMVEIPNRIMFSEMKRVTKALDLADMITRVIQEGLEGLVLKDVKGTYEPGKRHWLKV 422

    dssp: HHHH---E---EEE--EEEE--HHHHHHHHHHHHH-----EEEEE---------EEEEEE


    Query: 677 KKDYLNEGAMADTADLVVLGAFYGQGSKGGMMSIFLMGCYDPGSQKWCTVTKCAGGHDDA 736

    KKDYLNEGAMADTADLVVLGAFYGQGSKGGMMSIFLMGCYDPGSQKWCTVTKCAGGHDDA

    3l2p_A: 423 KKDYLNEGAMADTADLVVLGAFYGQGSKGGMMSIFLMGCYDPGSQKWCTVTKCAGGHDDA 482

    dssp: ------ --EEEEEEEEEEE-----------EEEEEEE------EEEEEEE-----HH


    Query: 737 TLARLQNELDMVKISKDPSKIPSWLKVNKIYYPDFIVPDPKKAAVWEITGAEFSKSEAHT 796

    TLARLQNELDMVKISKDPSKIPSWLKVNKIYYPDFIVPDPKKAAVWEITGAEFSKSEAHT

    3l2p_A: 483 TLARLQNELDMVKISKDPSKIPSWLKVNKIYYPDFIVPDPKKAAVWEITGAEFSKSEAHT 542

    dssp: HHHH------------ -EEEEEEE--EEE-----


    Query: 797 ADGISIRFPRCTRIRDDKDWKSATNLPQLKELYQLSK 833

    ADGISIRFPRCTRIRDDKDWKSATNLPQLKELYQLSK

    3l2p_A: 543 ADGISIRFPRCTRIRDDKDWKSATNLPQLKELYQLSK 579

    dssp: ---EEE---EE-------------EHHHHHHHHH---


    Download alignment FASTA file