Interaction between DNA ligase 1 (6p09_A) and DNA (6p09_D_B_C)

PDB and SCOP data

PDB ID: 6p09 (all binary interactions in this PDB entry)

Title: Human DNA Ligase 1 Bound to an Adenylated, dideoxy Terminated DNA nick with 200 mM Mg2+

Release date: 2019-12-11

Resolution: 2.1 Å

  • Chain A: 6p09_A

    Title: DNA ligase 1

    Source organism: Homo sapiens

    Number of residues: 645 (3 missing in structure)

  • Chain B: 6p09_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: 2298.78 Å2

Number of inter-residue contacts at the interface: 192

Number of H-bonds: 32

  • 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 6p09_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 303 44 S 41.5 39.3 %
    2 304 45 A 27.4 48.7 %
    3 305 46 R 85.2 61.0 %
    4 306 47 L 1.8 1.2 %
    5 346 87 E 44.2 49.9 %
    6 347 88 L 12.4 41.2 %
    7 348 89 G 27.9 59.5 %
    8 349 90 V 18.8 99.8 %
    9 350 91 G 25.6 82.1 %
    10 351 92 D 8.5 18.1 %
    11 352 93 G 16.3 40.0 %
    12 353 94 V 5.6 18.0 %
    13 356 97 K 11.5 11.9 %
    14 370 111 R 2.9 3.0 %
    15 414 155 L 1.4 3.0 %
    16 415 156 T 13.2 11.6 %
    17 416 157 G 27.2 50.7 %
    18 417 158 S 19.9 16.5 %
    19 418 159 A 17.6 26.4 %
    20 419 160 S 17.5 93.9 %
    21 420 161 T 37.0 55.1 %
    22 421 162 A 1.2 2.0 %
    23 423 164 K 0.3 2.2 %
    24 446 187 L 1.9 57.9 %
    25 447 188 S 3.0 16.7 %
    26 448 189 G 2.1 3.8 %
    27 449 190 R 29.8 27.8 %
    28 451 192 R 47.4 49.3 %
    29 452 193 L 5.4 42.9 %
    30 453 194 G 35.1 65.3 %
    31 454 195 L 13.6 76.2 %
    32 455 196 A 38.7 59.8 %
    33 456 197 E 5.0 11.4 %
    34 457 198 Q 48.9 55.0 %
    35 458 199 S 14.9 77.2 %
    36 504 245 K 16.9 29.8 %
    37 546 287 H 36.0 48.9 %
    38 547 288 P 4.0 5.9 %
    39 557 298 R 2.8 2.5 %
    40 568 309 K 2.6 92.3 %
    41 570 311 D 0.7 3.8 %
    42 571 312 G 8.6 100.0 %
    43 572 313 Q 36.9 79.6 %
    44 573 314 R 14.4 85.2 %
    45 588 329 S 21.4 91.4 %
    46 589 330 R 38.1 40.9 %
    47 590 331 N 32.3 32.4 %
    48 592 333 E 31.1 59.9 %
    49 594 335 N 5.4 20.0 %
    50 597 338 K 0.7 4.8 %
    51 621 362 E 0.5 100.0 %
    52 635 376 F 38.3 67.2 %
    53 636 377 Q 34.3 45.0 %
    54 639 380 T 42.0 64.1 %
    55 640 381 T 35.2 38.1 %
    56 641 382 R 9.1 46.3 %
    57 642 383 K 43.6 28.5 %
    58 643 384 R 97.2 57.2 %
    59 644 385 K 61.0 40.1 %
    60 720 461 E 0.3 1.3 %
    61 737 478 K 3.3 2.2 %
    62 738 479 R 45.3 31.2 %
    63 739 480 S 16.6 40.8 %
    64 740 481 H 8.8 13.9 %
    65 744 485 K 15.4 58.4 %
    66 746 487 K 12.0 83.1 %
    67 748 489 D 1.6 11.6 %
    68 749 490 Y 33.8 62.6 %
    69 765 506 Y 4.2 21.2 %
    70 766 507 L 2.4 4.8 %
    71 767 508 G 4.2 88.4 %
    72 768 509 R 31.1 43.3 %
    73 769 510 G 9.8 48.0 %
    74 770 511 K 84.7 46.5 %
    75 771 512 R 37.3 56.9 %
    76 776 517 G 19.4 98.0 %
    77 777 518 G 11.4 88.7 %
    78 778 519 F <0.1 86.0 %
    79 794 535 C 9.0 100.0 %
    80 795 536 K 63.0 69.5 %
    81 796 537 L 9.3 100.0 %
    82 797 538 G 34.6 99.5 %
    83 798 539 T 58.4 91.4 %
    84 799 540 G 23.8 95.4 %
    85 800 541 F 12.5 91.2 %
    86 801 542 S 28.9 54.5 %
    87 802 543 D 41.6 40.0 %
    88 803 544 E 1.8 1.4 %
    89 850 591 S 23.2 71.0 %
    90 851 592 L 8.6 20.4 %
    91 852 593 S 14.1 99.9 %
    92 853 594 P 37.7 36.1 %
    93 854 595 I 8.4 10.7 %
    94 855 596 Y 23.7 93.3 %
    95 866 607 K 10.0 11.7 %
    96 869 610 S 19.3 100.0 %
    97 870 611 L 13.5 100.0 %
    98 871 612 R 24.5 49.5 %
    99 872 613 F 85.2 95.3 %
    100 873 614 P 29.5 94.6 %
    101 874 615 R 49.2 96.6 %
    102 876 617 I 3.7 5.8 %

  • Interface residues in 6p09_D_B_C

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 9:D1 G 39.3 17.3 %
    2 2 10:D1 T 79.2 47.8 %
    3 3 11:D1 C 105.1 58.8 %
    4 4 12:D1 C 93.2 62.9 %
    5 5 13:D1 G 96.7 51.4 %
    6 6 14:D1 A 142.1 85.7 %
    7 7 15:D1 C 102.9 61.9 %
    8 8 16:D1 G 118.1 65.0 %
    9 9 17:D1 A 101.5 71.3 %
    10 10 18:D1 C 89.1 58.0 %
    11 11 19:D1 G 103.0 63.2 %
    12 12 20:D1 C 91.5 57.2 %
    13 13 21:D1 A 79.8 52.1 %
    14 14 22:D1 T 28.2 15.9 %
    15 15 23:D1 C 71.0 41.2 %
    16 16 24:D1 A 64.5 44.0 %
    17 17 25:D1 G 11.2 6.2 %
    18 24 8:B1 T 6.9 3.4 %
    19 25 9:B1 G 83.1 47.8 %
    20 26 10:B1 C 79.3 48.2 %
    21 27 11:B1 G 53.5 37.2 %
    22 28 12:B1 T 108.5 66.8 %
    23 29 13:B1 C 111.6 84.9 %
    24 30 1:C1 G 54.1 53.9 %
    25 31 2:C1 T 107.8 71.5 %
    26 32 3:C1 C 80.0 47.9 %
    27 33 4:C1 G 51.6 32.5 %
    28 34 5:C1 G 52.5 30.9 %
    29 35 6:C1 A 31.6 17.2 %
    30 36 7:C1 C 61.8 21.9 %

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 21.0 H-bond
3 304 45 A 36 7:C1 C 27.4
4 305 46 R 1 9:D1 G 3.5
5 305 46 R 2 10:D1 T 14.4
6 305 46 R 3 11:D1 C 37.7
7 305 46 R 4 12:D1 C 8.4
8 305 46 R 34 5:C1 G 0.5
9 305 46 R 35 6:C1 A 9.1
10 305 46 R 36 7:C1 C 11.6
11 306 47 L 36 7:C1 C 1.8
12 346 87 E 26 10:B1 C 33.3
13 346 87 E 27 11:B1 G 10.9
14 347 88 L 26 10:B1 C 12.4
15 348 89 G 25 9:B1 G 17.8
16 348 89 G 26 10:B1 C 10.1 H-bond
17 349 90 V 25 9:B1 G 14.6
18 349 90 V 26 10:B1 C 4.2
19 350 91 G 25 9:B1 G 16.7
20 350 91 G 26 10:B1 C 8.9
21 351 92 D 25 9:B1 G 8.5
22 352 93 G 24 8:B1 T 4.0
23 352 93 G 25 9:B1 G 12.3
24 353 94 V 25 9:B1 G 5.6
25 356 97 K 16 24:D1 A 0.2
26 356 97 K 17 25:D1 G 11.2
27 370 111 R 24 8:B1 T 2.9
28 414 155 L 15 23:D1 C 1.4
29 415 156 T 15 23:D1 C 13.2
30 416 157 G 15 23:D1 C 26.7 H-bond
31 416 157 G 16 24:D1 A 0.5
32 417 158 S 15 23:D1 C 6.7
33 417 158 S 16 24:D1 A 13.2
34 418 159 A 16 24:D1 A 17.6 H-bond
35 419 160 S 15 23:D1 C 13.2
36 419 160 S 16 24:D1 A 4.3
37 420 161 T 15 23:D1 C 9.6
38 420 161 T 16 24:D1 A 27.4 H-bond
39 421 162 A 16 24:D1 A 1.2
40 423 164 K 15 23:D1 C 0.3
41 446 187 L 26 10:B1 C 1.9
42 447 188 S 26 10:B1 C 3.0
43 448 189 G 26 10:B1 C 2.1
44 449 190 R 6 14:D1 A 15.5
45 449 190 R 7 15:D1 C 14.3 H-bond
46 451 192 R 5 13:D1 G 21.6
47 451 192 R 6 14:D1 A 25.7
48 452 193 L 5 13:D1 G 5.4
49 453 194 G 4 12:D1 C 19.3
50 453 194 G 5 13:D1 G 15.8 H-bond
51 454 195 L 4 12:D1 C 6.0
52 454 195 L 5 13:D1 G 7.6
53 455 196 A 4 12:D1 C 25.4 H-bond
54 455 196 A 5 13:D1 G 13.3
55 456 197 E 4 12:D1 C 5.0
56 457 198 Q 3 11:D1 C 35.0
57 457 198 Q 4 12:D1 C 13.9 H-bond
58 458 199 S 3 11:D1 C 3.3
59 458 199 S 4 12:D1 C 11.6 H-bond
60 504 245 K 3 11:D1 C 16.9 H-bond
61 546 287 H 1 9:D1 G 9.8
62 546 287 H 2 10:D1 T 26.2 H-bond
63 547 288 P 32 3:C1 C 4.0
64 557 298 R 1 9:D1 G 2.8
65 568 309 K 30 1:C1 G 2.6
66 570 311 D 29 13:B1 C 0.7
67 571 312 G 29 13:B1 C 8.6
68 572 313 Q 28 12:B1 T 27.7
69 572 313 Q 29 13:B1 C 9.2
70 573 314 R 28 12:B1 T 0.1
71 573 314 R 29 13:B1 C 14.2 H-bond
72 588 329 S 28 12:B1 T 20.5 H-bond
73 588 329 S 29 13:B1 C 0.9
74 589 330 R 28 12:B1 T <0.1
75 589 330 R 29 13:B1 C 22.7
76 589 330 R 30 1:C1 G 15.4
77 590 331 N 28 12:B1 T 26.2 H-bond
78 590 331 N 29 13:B1 C 6.1
79 592 333 E 27 11:B1 G 21.2
80 592 333 E 28 12:B1 T 9.9
81 594 335 N 28 12:B1 T 5.4
82 597 338 K 28 12:B1 T 0.7
83 621 362 E 29 13:B1 C 0.5
84 635 376 F 9 17:D1 A 4.9
85 635 376 F 28 12:B1 T 14.3
86 635 376 F 29 13:B1 C 19.1
87 636 377 Q 10 18:D1 C 12.8
88 636 377 Q 11 19:D1 G 21.4 H-bond
89 639 380 T 11 19:D1 G 30.2 H-bond
90 639 380 T 12 20:D1 C 6.9
91 639 380 T 27 11:B1 G 1.3
92 639 380 T 28 12:B1 T 3.6
93 640 381 T 11 19:D1 G 12.1
94 640 381 T 12 20:D1 C 23.1
95 641 382 R 12 20:D1 C 9.1
96 642 383 K 12 20:D1 C 22.5
97 642 383 K 13 21:D1 A 21.2
98 643 384 R 11 19:D1 G 10.3
99 643 384 R 12 20:D1 C 30.0 H-bond
100 643 384 R 13 21:D1 A 25.8 H-bond
101 643 384 R 25 9:B1 G 7.6
102 643 384 R 26 10:B1 C 3.3
103 643 384 R 27 11:B1 G 20.2
104 644 385 K 13 21:D1 A 32.8
105 644 385 K 14 22:D1 T 28.2
106 720 461 E 29 13:B1 C 0.3
107 737 478 K 2 10:D1 T 3.3
108 738 479 R 1 9:D1 G 23.3
109 738 479 R 2 10:D1 T 22.0 H-bond
110 739 480 S 2 10:D1 T 4.4
111 739 480 S 3 11:D1 C 12.2
112 740 481 H 2 10:D1 T 8.8
113 744 485 K 30 1:C1 G 0.2
114 744 485 K 31 2:C1 T 15.2 H-bond
115 746 487 K 30 1:C1 G 2.1
116 746 487 K 31 2:C1 T 10.0
117 748 489 D 31 2:C1 T 1.6
118 749 490 Y 31 2:C1 T 22.5 H-bond
119 749 490 Y 32 3:C1 C 11.3
120 765 506 Y 8 16:D1 G 4.2
121 766 507 L 7 15:D1 C 2.4
122 767 508 G 7 15:D1 C 4.2
123 768 509 R 6 14:D1 A 9.5 H-bond
124 768 509 R 7 15:D1 C 21.6 H-bond
125 769 510 G 6 14:D1 A 9.8
126 770 511 K 4 12:D1 C 3.5
127 770 511 K 5 13:D1 G 32.9
128 770 511 K 6 14:D1 A 37.3 H-bond
129 770 511 K 33 4:C1 G 10.0
130 770 511 K 34 5:C1 G 0.9
131 771 512 R 5 13:D1 G 0.1
132 771 512 R 6 14:D1 A 31.5
133 771 512 R 7 15:D1 C 3.6
134 771 512 R 33 4:C1 G 2.1
135 776 517 G 6 14:D1 A <0.1
136 776 517 G 7 15:D1 C 19.4
137 777 518 G 7 15:D1 C 6.9
138 777 518 G 8 16:D1 G 4.6
139 778 519 F 8 16:D1 G <0.1
140 794 535 C 8 16:D1 G 0.3
141 794 535 C 9 17:D1 A 8.7
142 795 536 K 8 16:D1 G 42.3 H-bond
143 795 536 K 9 17:D1 A 20.6 H-bond
144 796 537 L 7 15:D1 C 0.3
145 796 537 L 8 16:D1 G 9.0
146 797 538 G 6 14:D1 A 4.5
147 797 538 G 7 15:D1 C 22.5
148 797 538 G 8 16:D1 G 7.6
149 798 539 T 6 14:D1 A 8.3
150 798 539 T 7 15:D1 C 7.8
151 798 539 T 8 16:D1 G 3.3
152 798 539 T 30 1:C1 G 5.0
153 798 539 T 31 2:C1 T 17.0
154 798 539 T 32 3:C1 C 17.0
155 799 540 G 32 3:C1 C 16.0
156 799 540 G 33 4:C1 G 7.8
157 800 541 F 33 4:C1 G 12.5
158 801 542 S 33 4:C1 G 16.1
159 801 542 S 34 5:C1 G 12.9
160 802 543 D 33 4:C1 G 3.1
161 802 543 D 34 5:C1 G 36.3 H-bond
162 802 543 D 35 6:C1 A 2.1
163 803 544 E 34 5:C1 G 1.8
164 850 591 S 9 17:D1 A 6.2
165 850 591 S 10 18:D1 C 17.0 H-bond
166 851 592 L 10 18:D1 C 6.4
167 851 592 L 11 19:D1 G 2.2
168 852 593 S 10 18:D1 C 14.1 H-bond
169 853 594 P 10 18:D1 C 20.9
170 853 594 P 11 19:D1 G 16.8
171 854 595 I 9 17:D1 A 2.0
172 854 595 I 10 18:D1 C 6.5
173 855 596 Y 9 17:D1 A 19.0 H-bond
174 855 596 Y 10 18:D1 C 4.7
175 866 607 K 11 19:D1 G 10.0
176 869 610 S 9 17:D1 A 12.6
177 869 610 S 10 18:D1 C 6.8
178 870 611 L 9 17:D1 A 13.5
179 871 612 R 8 16:D1 G 3.2
180 871 612 R 9 17:D1 A 7.4
181 871 612 R 29 13:B1 C 13.9
182 872 613 F 8 16:D1 G 20.0
183 872 613 F 9 17:D1 A 1.4
184 872 613 F 29 13:B1 C 15.4
185 872 613 F 30 1:C1 G 28.9
186 872 613 F 31 2:C1 T 19.6
187 873 614 P 8 16:D1 G 23.5
188 873 614 P 9 17:D1 A 5.3
189 873 614 P 31 2:C1 T 0.7
190 874 615 R 31 2:C1 T 21.3
191 874 615 R 32 3:C1 C 27.9 H-bond
192 876 617 I 32 3:C1 C 3.7

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A6p09_A1001MG 48.818.1
A6p09_A1002MG 56.714.2
A6p09_A1003MG 41.319.6
B6p09_D_B_C101AMP 45.0301.7
B6p09_D_B_C102MG 25.940.2

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

    Result domain: 6p09_A; DNA ligase 1

    Alignment data:

    Expectation value = 5.93e-48, Score = 185 bits (469),

    Identities = 33% (124/373), Positive = 50% (188/373), Gaps = 9% (35/373).

    Interface alignment data:

    Interface residues in alignment: 65% (66/102).

    Identities = 44% (29/66), Positive = 59% (39/66), Gaps = 5% (3/66).

    Query: 480 PVQPMLAEACKSVEYAMKKCPNGMFS-EIKYDGERVQVHK-NGDHFSYFSRSLKPVLPHK 537

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

    6p09_A: 280 PLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQE----DN 335

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


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

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

    6p09_A: 336 TGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQ 395

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


    Query: 590 VCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIPNRIMFSEMKRVTKALDLADMITRV 649

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

    6p09_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 +

    6p09_A: 456 VKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLD--GVGDTLDLVVIGAYLGRGKRA 513

    dssp: HH----EEEEEE---------------EEEEEHHH-- ----EEEEEEEEEEEE-HHHE


    Query: 706 GMMSIFLMGCYDPGSQKWCTVTKCAGGHDDATLARLQNELDMVKISKDPSKIPSWLKVNK 765

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

    6p09_A: 514 GRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVL---PSPRP-YVRIDG 569

    dssp: --EEEEEEEEEE----EEEEEEEE-----HHHHHHHHHHHHHHEE ----- -EE---


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

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

    6p09_A: 570 AVIPDHWL-DP--SAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPE 626

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


    Query: 818 SATNLPQLKELYQ 830

    AT Q+ LY+

    6p09_A: 627 QATTSAQVACLYR 639

    dssp: H--EHHHHHHHHH


    Download alignment FASTA file