Interaction between DNA ligase 1 (6p0b_A) and DNA (6p0b_D_B_C)

PDB and SCOP data

PDB ID: 6p0b (all binary interactions in this PDB entry)

Title: Human DNA Ligase 1 (E346A/E592A) Bound to an Adenylated, dideoxy Terminated DNA nick with 200 mM Mg2+

Release date: 2019-12-11

Resolution: 2.2 Å

  • Chain A: 6p0b_A

    Title: DNA ligase 1

    Source organism: Homo sapiens

    Number of residues: 645 (3 missing in structure)

  • Chain B: 6p0b_D_B_C

    Title: DNA

    Source organism: synthetic construct

    Number of residues: 36

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

Buried interface area: 2324.66 Å2

Number of inter-residue contacts at the interface: 194

Number of H-bonds: 34

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Homomer, 1 protein, 1 nucleic acid.

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Create a structural model for this interaction

  • Interface residues in 6p0b_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 303 44 S 41.9 39.6 %
    2 304 45 A 27.3 48.9 %
    3 305 46 R 85.0 59.7 %
    4 306 47 L 4.8 3.1 %
    5 344 85 G 10.3 17.2 %
    6 345 86 L 3.9 7.0 %
    7 346 87 A 33.5 54.3 %
    8 347 88 L 6.4 20.9 %
    9 348 89 G 29.0 52.2 %
    10 349 90 V 16.9 88.7 %
    11 350 91 G 23.0 63.8 %
    12 351 92 D 7.6 13.9 %
    13 352 93 G 11.0 29.7 %
    14 353 94 V 0.9 2.9 %
    15 356 97 K 7.4 7.9 %
    16 370 111 R 0.5 0.5 %
    17 414 155 L 0.7 1.6 %
    18 415 156 T 13.7 11.7 %
    19 416 157 G 31.0 57.1 %
    20 417 158 S 23.4 19.2 %
    21 418 159 A 16.5 23.1 %
    22 419 160 S 15.4 83.3 %
    23 420 161 T 37.9 58.8 %
    24 421 162 A 0.5 0.8 %
    25 423 164 K 1.5 10.6 %
    26 449 190 R 34.4 30.9 %
    27 451 192 R 48.4 46.7 %
    28 452 193 L 5.2 44.8 %
    29 453 194 G 34.6 63.6 %
    30 454 195 L 14.4 79.4 %
    31 455 196 A 39.6 62.3 %
    32 456 197 E 5.0 11.4 %
    33 457 198 Q 48.1 53.4 %
    34 458 199 S 14.8 75.2 %
    35 504 245 K 14.9 30.7 %
    36 546 287 H 35.0 54.4 %
    37 547 288 P 3.7 5.4 %
    38 557 298 R 23.1 22.1 %
    39 568 309 K 2.5 100.0 %
    40 570 311 D 0.7 3.4 %
    41 571 312 G 8.8 100.0 %
    42 572 313 Q 36.3 67.9 %
    43 573 314 R 14.5 78.6 %
    44 588 329 S 21.4 89.0 %
    45 589 330 R 40.2 42.7 %
    46 590 331 N 31.1 30.1 %
    47 592 333 A 20.7 51.6 %
    48 594 335 N 13.6 54.5 %
    49 597 338 K 11.3 45.3 %
    50 621 362 E 0.9 100.0 %
    51 635 376 F 37.8 68.7 %
    52 636 377 Q 36.5 46.8 %
    53 639 380 T 42.8 64.6 %
    54 640 381 T 39.7 42.2 %
    55 641 382 R 9.4 35.9 %
    56 642 383 K 42.9 28.0 %
    57 643 384 R 103.5 63.3 %
    58 644 385 K 58.8 36.9 %
    59 720 461 E 0.3 1.2 %
    60 737 478 K 3.5 2.4 %
    61 738 479 R 47.5 33.2 %
    62 739 480 S 16.1 38.6 %
    63 740 481 H 9.4 15.4 %
    64 744 485 K 16.4 68.0 %
    65 746 487 K 8.3 51.6 %
    66 748 489 D 1.4 9.1 %
    67 749 490 Y 33.9 53.5 %
    68 765 506 Y 4.0 19.5 %
    69 766 507 L 2.7 5.8 %
    70 767 508 G 4.1 83.9 %
    71 768 509 R 29.6 41.5 %
    72 769 510 G 9.3 44.3 %
    73 770 511 K 82.3 45.5 %
    74 771 512 R 40.7 60.6 %
    75 776 517 G 18.7 98.3 %
    76 777 518 G 11.2 88.2 %
    77 778 519 F <0.1 66.4 %
    78 794 535 C 8.4 100.0 %
    79 795 536 K 64.8 70.1 %
    80 796 537 L 8.4 100.0 %
    81 797 538 G 34.7 99.7 %
    82 798 539 T 59.1 90.7 %
    83 799 540 G 23.1 95.9 %
    84 800 541 F 12.1 88.9 %
    85 801 542 S 29.0 56.7 %
    86 802 543 D 42.1 39.8 %
    87 803 544 E 3.1 2.2 %
    88 850 591 S 23.7 68.9 %
    89 851 592 L 8.9 20.5 %
    90 852 593 S 13.9 100.0 %
    91 853 594 P 38.0 36.8 %
    92 854 595 I 8.4 10.8 %
    93 855 596 Y 23.6 96.6 %
    94 866 607 K 12.1 14.3 %
    95 869 610 S 20.0 100.0 %
    96 870 611 L 13.6 100.0 %
    97 871 612 R 21.2 40.1 %
    98 872 613 F 90.2 95.5 %
    99 873 614 P 28.9 93.7 %
    100 874 615 R 49.7 98.0 %
    101 876 617 I 3.9 5.9 %

  • Interface residues in 6p0b_D_B_C

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 9:D1 G 57.0 25.3 %
    2 2 10:D1 T 83.2 50.1 %
    3 3 11:D1 C 102.0 56.5 %
    4 4 12:D1 C 93.7 63.7 %
    5 5 13:D1 G 99.6 52.5 %
    6 6 14:D1 A 144.7 87.2 %
    7 7 15:D1 C 103.6 61.7 %
    8 8 16:D1 G 115.1 63.5 %
    9 9 17:D1 A 100.1 69.2 %
    10 10 18:D1 C 94.9 62.0 %
    11 11 19:D1 G 108.0 64.9 %
    12 12 20:D1 C 86.6 52.9 %
    13 13 21:D1 A 79.6 55.5 %
    14 14 22:D1 T 28.8 15.4 %
    15 15 23:D1 C 73.8 47.6 %
    16 16 24:D1 A 66.9 44.1 %
    17 17 25:D1 G 7.4 4.1 %
    18 24 8:B1 T 3.2 1.6 %
    19 25 9:B1 G 71.1 47.0 %
    20 26 10:B1 C 62.1 37.4 %
    21 27 11:B1 G 57.2 31.4 %
    22 28 12:B1 T 130.4 74.2 %
    23 29 13:B1 C 110.2 83.7 %
    24 30 1:C1 G 54.7 54.5 %
    25 31 2:C1 T 107.7 70.9 %
    26 32 3:C1 C 81.3 48.5 %
    27 33 4:C1 G 51.6 32.8 %
    28 34 5:C1 G 52.9 31.5 %
    29 35 6:C1 A 31.7 17.2 %
    30 36 7:C1 C 65.8 23.2 %

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
1 303 44 S 35 6:C1 A 20.5
2 303 44 S 36 7:C1 C 21.5 H-bond
3 304 45 A 36 7:C1 C 27.3
4 305 46 R 1 9:D1 G 3.5
5 305 46 R 2 10:D1 T 14.3
6 305 46 R 3 11:D1 C 37.6
7 305 46 R 4 12:D1 C 7.9
8 305 46 R 34 5:C1 G 0.4
9 305 46 R 35 6:C1 A 9.0
10 305 46 R 36 7:C1 C 12.3
11 306 47 L 36 7:C1 C 4.8
12 344 85 G 27 11:B1 G 10.3
13 345 86 L 27 11:B1 G 3.9
14 346 87 A 26 10:B1 C 24.9
15 346 87 A 27 11:B1 G 8.6
16 347 88 L 26 10:B1 C 6.4
17 348 89 G 25 9:B1 G 13.8
18 348 89 G 26 10:B1 C 15.2 H-bond
19 349 90 V 25 9:B1 G 13.8
20 349 90 V 26 10:B1 C 3.1
21 350 91 G 25 9:B1 G 19.1
22 350 91 G 26 10:B1 C 3.9
23 351 92 D 25 9:B1 G 7.6
24 352 93 G 24 8:B1 T 2.8
25 352 93 G 25 9:B1 G 8.3
26 353 94 V 25 9:B1 G 0.9
27 356 97 K 17 25:D1 G 7.4
28 370 111 R 24 8:B1 T 0.5
29 414 155 L 15 23:D1 C 0.7
30 415 156 T 15 23:D1 C 13.7
31 416 157 G 15 23:D1 C 30.0 H-bond
32 416 157 G 16 24:D1 A 1.1
33 417 158 S 15 23:D1 C 8.3
34 417 158 S 16 24:D1 A 15.2
35 418 159 A 16 24:D1 A 16.5 H-bond
36 419 160 S 15 23:D1 C 10.8
37 419 160 S 16 24:D1 A 4.6
38 420 161 T 15 23:D1 C 8.8
39 420 161 T 16 24:D1 A 29.1 H-bond
40 421 162 A 16 24:D1 A 0.5
41 423 164 K 15 23:D1 C 1.5
42 449 190 R 6 14:D1 A 18.7
43 449 190 R 7 15:D1 C 15.7 H-bond
44 451 192 R 5 13:D1 G 23.3
45 451 192 R 6 14:D1 A 25.1
46 452 193 L 5 13:D1 G 5.2
47 453 194 G 4 12:D1 C 19.1
48 453 194 G 5 13:D1 G 15.5 H-bond
49 454 195 L 4 12:D1 C 6.2
50 454 195 L 5 13:D1 G 8.2
51 455 196 A 4 12:D1 C 26.0 H-bond
52 455 196 A 5 13:D1 G 13.5
53 456 197 E 4 12:D1 C 5.0
54 457 198 Q 3 11:D1 C 33.8
55 457 198 Q 4 12:D1 C 14.3 H-bond
56 458 199 S 3 11:D1 C 3.4
57 458 199 S 4 12:D1 C 11.4 H-bond
58 504 245 K 3 11:D1 C 14.9
59 546 287 H 1 9:D1 G 6.7
60 546 287 H 2 10:D1 T 28.2 H-bond
61 547 288 P 32 3:C1 C 3.7
62 557 298 R 1 9:D1 G 23.1
63 557 298 R 2 10:D1 T <0.1
64 568 309 K 30 1:C1 G 2.5
65 570 311 D 29 13:B1 C 0.7
66 571 312 G 29 13:B1 C 8.8
67 572 313 Q 28 12:B1 T 27.4
68 572 313 Q 29 13:B1 C 8.9
69 573 314 R 28 12:B1 T <0.1
70 573 314 R 29 13:B1 C 14.5 H-bond
71 588 329 S 28 12:B1 T 21.1 H-bond
72 588 329 S 29 13:B1 C 0.3
73 589 330 R 28 12:B1 T 1.4
74 589 330 R 29 13:B1 C 24.2
75 589 330 R 30 1:C1 G 14.6
76 590 331 N 27 11:B1 G 3.2
77 590 331 N 28 12:B1 T 24.3 H-bond
78 590 331 N 29 13:B1 C 3.6
79 592 333 A 27 11:B1 G 6.4
80 592 333 A 28 12:B1 T 14.3
81 594 335 N 28 12:B1 T 13.6 H-bond
82 597 338 K 27 11:B1 G 0.1
83 597 338 K 28 12:B1 T 11.2
84 621 362 E 29 13:B1 C 0.9
85 635 376 F 9 17:D1 A 4.7
86 635 376 F 28 12:B1 T 13.4
87 635 376 F 29 13:B1 C 19.7
88 636 377 Q 10 18:D1 C 17.2
89 636 377 Q 11 19:D1 G 19.4 H-bond
90 639 380 T 10 18:D1 C 2.9
91 639 380 T 11 19:D1 G 28.3 H-bond
92 639 380 T 12 20:D1 C 7.0
93 639 380 T 27 11:B1 G 0.9
94 639 380 T 28 12:B1 T 3.7
95 640 381 T 11 19:D1 G 15.0
96 640 381 T 12 20:D1 C 24.7
97 641 382 R 12 20:D1 C 9.4
98 642 383 K 12 20:D1 C 21.3
99 642 383 K 13 21:D1 A 21.6
100 643 384 R 11 19:D1 G 11.3
101 643 384 R 12 20:D1 C 24.2 H-bond
102 643 384 R 13 21:D1 A 28.1 H-bond
103 643 384 R 25 9:B1 G 7.7
104 643 384 R 26 10:B1 C 8.6
105 643 384 R 27 11:B1 G 23.7
106 644 385 K 13 21:D1 A 30.0
107 644 385 K 14 22:D1 T 28.8
108 720 461 E 29 13:B1 C 0.3
109 737 478 K 2 10:D1 T 3.5
110 738 479 R 1 9:D1 G 23.7
111 738 479 R 2 10:D1 T 23.9 H-bond
112 739 480 S 2 10:D1 T 3.9
113 739 480 S 3 11:D1 C 12.3
114 740 481 H 2 10:D1 T 9.4
115 744 485 K 30 1:C1 G <0.1
116 744 485 K 31 2:C1 T 16.4 H-bond
117 746 487 K 30 1:C1 G 0.3
118 746 487 K 31 2:C1 T 8.0
119 748 489 D 31 2:C1 T 1.4
120 749 490 Y 31 2:C1 T 21.4 H-bond
121 749 490 Y 32 3:C1 C 12.5
122 765 506 Y 8 16:D1 G 4.0
123 766 507 L 7 15:D1 C 2.7
124 767 508 G 7 15:D1 C 4.1
125 768 509 R 6 14:D1 A 9.2 H-bond
126 768 509 R 7 15:D1 C 20.4 H-bond
127 769 510 G 6 14:D1 A 9.3
128 770 511 K 4 12:D1 C 3.7
129 770 511 K 5 13:D1 G 31.6 H-bond
130 770 511 K 6 14:D1 A 36.9 H-bond
131 770 511 K 33 4:C1 G 10.1
132 771 512 R 5 13:D1 G 2.3
133 771 512 R 6 14:D1 A 31.8
134 771 512 R 7 15:D1 C 4.0
135 771 512 R 33 4:C1 G 2.6
136 776 517 G 6 14:D1 A <0.1
137 776 517 G 7 15:D1 C 18.7
138 777 518 G 7 15:D1 C 7.5
139 777 518 G 8 16:D1 G 3.6
140 778 519 F 8 16:D1 G <0.1
141 794 535 C 8 16:D1 G 0.2
142 794 535 C 9 17:D1 A 8.3
143 795 536 K 8 16:D1 G 43.3 H-bond
144 795 536 K 9 17:D1 A 21.5 H-bond
145 796 537 L 7 15:D1 C 0.4
146 796 537 L 8 16:D1 G 8.0
147 797 538 G 6 14:D1 A 4.7
148 797 538 G 7 15:D1 C 22.3
149 797 538 G 8 16:D1 G 7.8
150 798 539 T 6 14:D1 A 9.0
151 798 539 T 7 15:D1 C 7.8
152 798 539 T 8 16:D1 G 2.9
153 798 539 T 30 1:C1 G 5.2
154 798 539 T 31 2:C1 T 16.7 H-bond
155 798 539 T 32 3:C1 C 17.5
156 798 539 T 33 4:C1 G <0.1
157 799 540 G 32 3:C1 C 15.7
158 799 540 G 33 4:C1 G 7.4
159 800 541 F 33 4:C1 G 12.1
160 801 542 S 33 4:C1 G 17.1
161 801 542 S 34 5:C1 G 11.9
162 802 543 D 33 4:C1 G 2.3
163 802 543 D 34 5:C1 G 37.6 H-bond
164 802 543 D 35 6:C1 A 2.2
165 803 544 E 34 5:C1 G 3.1
166 850 591 S 9 17:D1 A 5.3
167 850 591 S 10 18:D1 C 18.4 H-bond
168 851 592 L 10 18:D1 C 6.5
169 851 592 L 11 19:D1 G 2.3
170 852 593 S 10 18:D1 C 13.9 H-bond
171 853 594 P 10 18:D1 C 18.4
172 853 594 P 11 19:D1 G 19.7
173 854 595 I 9 17:D1 A 2.0
174 854 595 I 10 18:D1 C 6.3
175 855 596 Y 9 17:D1 A 19.2 H-bond
176 855 596 Y 10 18:D1 C 4.3
177 866 607 K 11 19:D1 G 12.1
178 869 610 S 9 17:D1 A 13.0
179 869 610 S 10 18:D1 C 7.0
180 870 611 L 9 17:D1 A 13.6
181 871 612 R 8 16:D1 G 2.5
182 871 612 R 9 17:D1 A 5.6
183 871 612 R 29 13:B1 C 13.1
184 872 613 F 8 16:D1 G 20.1
185 872 613 F 9 17:D1 A 1.5
186 872 613 F 29 13:B1 C 15.2
187 872 613 F 30 1:C1 G 32.1
188 872 613 F 31 2:C1 T 21.3
189 873 614 P 8 16:D1 G 22.8
190 873 614 P 9 17:D1 A 5.4
191 873 614 P 31 2:C1 T 0.8
192 874 615 R 31 2:C1 T 21.8
193 874 615 R 32 3:C1 C 27.9 H-bond
194 876 617 I 32 3:C1 C 3.9

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A6p0b_A1001MG 42.625.4
A6p0b_A1002MG 39.721.0
B6p0b_D_B_C101AMP 46.5302.6

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

    Result domain: 6p0b_A; DNA ligase 1

    Alignment data:

    Expectation value = 9.87e-48, Score = 184 bits (467),

    Identities = 33% (124/373), Positive = 50% (187/373), Gaps = 9% (35/373).

    Interface alignment data:

    Interface residues in alignment: 65% (66/101).

    Identities = 44% (29/66), Positive = 58% (38/66), Gaps = 5% (3/66).

    Query: 480 PVQPMLAEACKSVEYAMKKCPNGMFS-EIKYDGERVQVHK-NGDHFSYFSRSLKPVLPHK 537

    P++PMLA + + +K+ F+ E KYDG+R Q+H G FSR+

    6p0b_A: 280 PLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQA----DN 335

    dssp: ------EEE---HHHHHHHH----EEEEEE---EEEEEEE-----EEEE----- E-


    Query: 538 VAHFKDYIPQA----FPGGHSMILDSEVLLIDNKTGKPLPFGTLGVHKK----AAFQDAN 589

    + D I + P S ILD+E + D + + PF L K+ A+

    6p0b_A: 336 TGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQ 395

    dssp: HHH-HHHHHHHHHHE------EEEEEEEEEEE----EE--HHHH---------HHH---E


    Query: 590 VCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIPNRIMFSEMKRVTKALDLADMITRV 649

    VCL+ FD IY N SL+ PL RR+ L +N VE +F+ +A+ + +

    6p0b_A: 396 VCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQS 455

    dssp: EEEEEEEEEEE--EE-----HHHHHHHHHHHE--E---EEE--EEE---HHHHHHHHHHH


    Query: 650 IQEGLEGLVLK--DVKGTYEPGKR--HWLKVKKDYLNEGAMADTADLVVLGAFYGQGSKG 705

    +++ EGL++K DV TYE KR +WLK+KKDYL+ + DT DLVV+GA+ G+G +

    6p0b_A: 456 VKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLD--GVGDTLDLVVIGAYLGRGKRA 513

    dssp: HH----EEEEEE---------------EEEEEHHH-- ---EEEEEEEEEEEE--HHH-


    Query: 706 GMMSIFLMGCYDPGSQKWCTVTKCAGGHDDATLARLQNELDMVKISKDPSKIPSWLKVNK 765

    G FL+ YD S++ + K G D L L + + PS P +++++

    6p0b_A: 514 GRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVL---PSPRP-YVRIDG 569

    dssp: --EEEEEEEEEE----EEEEEEEE-----HHHHHHHHHHH---EE ----- -EE---


    Query: 766 IYYPDFIVPDPKKAAVWEITGAEFSKSEAHTA--------DGISIRFPRCTRIRDDKDWK 817

    PD + DP +AVWE+ A+ S S + A GIS+RFPR R+R+DK +

    6p0b_A: 570 AVIPDHWL-DP--SAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPE 626

    dssp: -----EEE -- --EEEEEE-EEEEE--------------EEEEE--EEEEE-----HH


    Query: 818 SATNLPQLKELYQ 830

    AT Q+ LY+

    6p0b_A: 627 QATTSAQVACLYR 639

    dssp: H--EHHHHHHHHH


    Download alignment FASTA file