Interaction between DNA ligase 1 (6p0d_A) and DNA (6p0d_D_B_C)

PDB and SCOP data

PDB ID: 6p0d (all binary interactions in this PDB entry)

Title: Human DNA Ligase 1 (E346A/E592A) Bound to an Adenylated, hydroxyl terminated DNA nick

Release date: 2019-12-11

Resolution: 1.8 Å

  • Chain A: 6p0d_A

    Title: DNA ligase 1

    Source organism: Homo sapiens

    Number of residues: 645 (4 missing in structure)

  • Chain B: 6p0d_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: 2388.95 Å2

Number of inter-residue contacts at the interface: 203

Number of H-bonds: 38

  • 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 6p0d_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 303 44 S 43.2 40.4 %
    2 304 45 A 25.5 46.1 %
    3 305 46 R 51.5 42.4 %
    4 306 47 L 5.8 4.0 %
    5 344 85 G 11.3 19.0 %
    6 345 86 L 3.6 6.3 %
    7 346 87 A 32.5 53.7 %
    8 347 88 L 9.4 31.7 %
    9 348 89 G 29.4 52.5 %
    10 349 90 V 19.8 86.1 %
    11 350 91 G 25.7 73.1 %
    12 351 92 D 6.5 13.5 %
    13 352 93 G 19.6 45.8 %
    14 353 94 V 13.0 37.1 %
    15 356 97 K 10.2 10.5 %
    16 370 111 R 6.8 6.7 %
    17 414 155 L 1.2 2.7 %
    18 415 156 T 14.7 12.4 %
    19 416 157 G 28.1 53.5 %
    20 417 158 S 15.9 13.7 %
    21 418 159 A 17.8 25.3 %
    22 419 160 S 16.3 94.0 %
    23 420 161 T 38.0 58.3 %
    24 421 162 A 1.1 1.8 %
    25 423 164 K 2.1 16.2 %
    26 449 190 R 34.4 30.9 %
    27 451 192 R 45.6 46.8 %
    28 452 193 L 5.7 49.7 %
    29 453 194 G 34.6 63.3 %
    30 454 195 L 14.2 76.9 %
    31 455 196 A 39.3 60.4 %
    32 456 197 E 5.0 11.2 %
    33 457 198 Q 51.6 56.6 %
    34 458 199 S 12.7 100.0 %
    35 504 245 K 13.0 23.4 %
    36 546 287 H 18.7 31.1 %
    37 547 288 P 7.3 13.5 %
    38 549 290 R 27.4 20.5 %
    39 557 298 R 30.4 38.8 %
    40 568 309 K 8.9 95.6 %
    41 570 311 D 2.5 13.2 %
    42 571 312 G 12.8 99.8 %
    43 572 313 Q 29.3 72.1 %
    44 573 314 R 13.6 87.2 %
    45 588 329 S 20.9 91.8 %
    46 589 330 R 43.7 45.0 %
    47 590 331 N 29.0 27.1 %
    48 592 333 A 20.5 51.5 %
    49 594 335 N 15.1 64.0 %
    50 597 338 K 10.8 45.3 %
    51 621 362 E 4.1 87.7 %
    52 635 376 F 41.9 70.2 %
    53 636 377 Q 38.9 51.6 %
    54 639 380 T 46.7 64.6 %
    55 640 381 T 40.0 44.2 %
    56 641 382 R 9.3 38.9 %
    57 642 383 K 44.1 33.1 %
    58 643 384 R 118.2 73.8 %
    59 644 385 K 48.5 29.1 %
    60 646 387 V <0.1 0.0 %
    61 720 461 E 8.5 25.8 %
    62 737 478 K 3.7 2.5 %
    63 738 479 R 45.8 35.9 %
    64 739 480 S 15.7 40.6 %
    65 740 481 H 15.2 19.9 %
    66 744 485 K 19.4 69.0 %
    67 746 487 K 16.1 84.3 %
    68 748 489 D 2.0 12.8 %
    69 749 490 Y 27.3 93.0 %
    70 765 506 Y 3.6 13.3 %
    71 766 507 L 2.7 5.6 %
    72 767 508 G 3.6 85.4 %
    73 768 509 R 29.7 36.4 %
    74 769 510 G 9.3 52.8 %
    75 770 511 K 81.0 45.9 %
    76 771 512 R 39.6 59.9 %
    77 776 517 G 19.6 98.0 %
    78 777 518 G 10.9 88.9 %
    79 778 519 F <0.1 100.0 %
    80 794 535 C 8.9 100.0 %
    81 795 536 K 64.7 69.7 %
    82 796 537 L 8.3 100.0 %
    83 797 538 G 35.8 99.7 %
    84 798 539 T 58.6 92.0 %
    85 799 540 G 34.4 88.1 %
    86 800 541 F 12.0 92.2 %
    87 801 542 S 28.2 51.0 %
    88 802 543 D 41.9 39.4 %
    89 803 544 E 1.7 1.3 %
    90 804 545 E 0.4 0.7 %
    91 845 586 K 0.7 6.1 %
    92 850 591 S 23.6 72.0 %
    93 851 592 L 9.0 21.8 %
    94 852 593 S 14.9 99.8 %
    95 853 594 P 37.1 36.5 %
    96 854 595 I 4.0 5.1 %
    97 855 596 Y 25.7 74.8 %
    98 866 607 K 13.5 15.9 %
    99 869 610 S 18.8 100.0 %
    100 870 611 L 12.8 100.0 %
    101 871 612 R 24.1 46.2 %
    102 872 613 F 87.4 95.2 %
    103 873 614 P 29.0 95.0 %
    104 874 615 R 47.5 99.6 %
    105 875 616 F 0.1 2.4 %
    106 876 617 I 4.6 6.4 %

  • Interface residues in 6p0d_D_B_C

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 9:D1 G 50.4 21.9 %
    2 2 10:D1 T 66.5 40.2 %
    3 3 11:D1 C 103.0 59.9 %
    4 4 12:D1 C 93.2 63.3 %
    5 5 13:D1 G 96.7 51.6 %
    6 6 14:D1 A 142.5 88.3 %
    7 7 15:D1 C 102.5 61.7 %
    8 8 16:D1 G 117.6 65.9 %
    9 9 17:D1 A 99.3 68.3 %
    10 10 18:D1 C 95.1 62.5 %
    11 11 19:D1 G 112.9 65.7 %
    12 12 20:D1 C 87.8 54.6 %
    13 13 21:D1 A 69.2 48.3 %
    14 14 22:D1 T 25.3 13.1 %
    15 15 23:D1 C 74.6 44.5 %
    16 16 24:D1 A 60.7 41.5 %
    17 17 25:D1 G 10.2 5.6 %
    18 24 8:B1 T 18.1 8.9 %
    19 25 9:B1 G 77.4 48.9 %
    20 26 10:B1 C 64.1 38.5 %
    21 27 11:B1 G 71.7 37.8 %
    22 28 12:B1 T 137.4 74.9 %
    23 29 13:B1 C 129.1 84.6 %
    24 30 1:C1 G 72.2 61.5 %
    25 31 2:C1 T 113.9 75.3 %
    26 32 3:C1 C 102.7 65.3 %
    27 33 4:C1 G 64.8 33.7 %
    28 34 5:C1 G 50.6 29.8 %
    29 35 6:C1 A 21.9 12.2 %
    30 36 7:C1 C 57.5 20.4 %

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 21.7
2 303 44 S 36 7:C1 C 21.6 H-bond
3 304 45 A 36 7:C1 C 25.5
4 305 46 R 2 10:D1 T 2.2
5 305 46 R 3 11:D1 C 36.0
6 305 46 R 4 12:D1 C 8.6
7 305 46 R 36 7:C1 C 4.6
8 306 47 L 36 7:C1 C 5.8
9 344 85 G 27 11:B1 G 11.3
10 345 86 L 27 11:B1 G 3.6
11 346 87 A 26 10:B1 C 21.2
12 346 87 A 27 11:B1 G 11.2
13 347 88 L 26 10:B1 C 9.4
14 348 89 G 25 9:B1 G 17.6
15 348 89 G 26 10:B1 C 11.8 H-bond
16 349 90 V 25 9:B1 G 6.3
17 349 90 V 26 10:B1 C 13.5
18 350 91 G 25 9:B1 G 23.5
19 350 91 G 26 10:B1 C 2.2
20 351 92 D 25 9:B1 G 6.5
21 352 93 G 24 8:B1 T 9.0
22 352 93 G 25 9:B1 G 10.6 H-bond
23 353 94 V 24 8:B1 T 2.3
24 353 94 V 25 9:B1 G 10.7
25 356 97 K 17 25:D1 G 10.2
26 370 111 R 24 8:B1 T 6.8
27 414 155 L 15 23:D1 C 1.2
28 415 156 T 15 23:D1 C 14.7
29 416 157 G 15 23:D1 C 27.6 H-bond
30 416 157 G 16 24:D1 A 0.6
31 417 158 S 15 23:D1 C 6.6
32 417 158 S 16 24:D1 A 9.3
33 418 159 A 16 24:D1 A 17.8 H-bond
34 419 160 S 15 23:D1 C 12.2
35 419 160 S 16 24:D1 A 4.1
36 420 161 T 15 23:D1 C 10.3
37 420 161 T 16 24:D1 A 27.8 H-bond
38 421 162 A 16 24:D1 A 1.1
39 423 164 K 15 23:D1 C 2.1
40 449 190 R 6 14:D1 A 19.3
41 449 190 R 7 15:D1 C 15.1 H-bond
42 451 192 R 5 13:D1 G 19.7
43 451 192 R 6 14:D1 A 25.9 H-bond
44 452 193 L 5 13:D1 G 5.7
45 453 194 G 4 12:D1 C 19.0
46 453 194 G 5 13:D1 G 15.5 H-bond
47 454 195 L 4 12:D1 C 5.8
48 454 195 L 5 13:D1 G 8.4
49 455 196 A 4 12:D1 C 25.6 H-bond
50 455 196 A 5 13:D1 G 13.7
51 456 197 E 4 12:D1 C 5.0
52 457 198 Q 3 11:D1 C 37.9
53 457 198 Q 4 12:D1 C 13.7 H-bond
54 458 199 S 3 11:D1 C 1.3
55 458 199 S 4 12:D1 C 11.4 H-bond
56 504 245 K 3 11:D1 C 13.0
57 546 287 H 1 9:D1 G 4.6
58 546 287 H 2 10:D1 T 14.1
59 547 288 P 31 2:C1 T 3.3
60 547 288 P 32 3:C1 C 4.0
61 549 290 R 32 3:C1 C 27.4 H-bond
62 557 298 R 1 9:D1 G 24.9
63 557 298 R 2 10:D1 T 5.4
64 568 309 K 29 13:B1 C 0.6
65 568 309 K 30 1:C1 G 8.2 H-bond
66 570 311 D 29 13:B1 C 2.5
67 571 312 G 29 13:B1 C 12.8
68 572 313 Q 28 12:B1 T 19.5
69 572 313 Q 29 13:B1 C 9.8
70 573 314 R 28 12:B1 T <0.1
71 573 314 R 29 13:B1 C 13.6 H-bond
72 588 329 S 28 12:B1 T 20.7 H-bond
73 588 329 S 29 13:B1 C 0.2
74 589 330 R 28 12:B1 T 0.9
75 589 330 R 29 13:B1 C 22.9
76 589 330 R 30 1:C1 G 19.9
77 590 331 N 27 11:B1 G 1.5
78 590 331 N 28 12:B1 T 21.8 H-bond
79 590 331 N 29 13:B1 C 5.7
80 592 333 A 27 11:B1 G 5.2
81 592 333 A 28 12:B1 T 15.3
82 594 335 N 28 12:B1 T 15.1 H-bond
83 597 338 K 28 12:B1 T 10.8
84 621 362 E 29 13:B1 C 3.9
85 621 362 E 30 1:C1 G 0.3
86 635 376 F 9 17:D1 A 5.4
87 635 376 F 10 18:D1 C 0.3
88 635 376 F 28 12:B1 T 16.5
89 635 376 F 29 13:B1 C 19.7
90 636 377 Q 10 18:D1 C 18.2
91 636 377 Q 11 19:D1 G 20.7 H-bond
92 639 380 T 10 18:D1 C 4.7
93 639 380 T 11 19:D1 G 26.8 H-bond
94 639 380 T 12 20:D1 C 7.6
95 639 380 T 27 11:B1 G 1.9
96 639 380 T 28 12:B1 T 5.5
97 640 381 T 11 19:D1 G 16.8
98 640 381 T 12 20:D1 C 23.2
99 641 382 R 12 20:D1 C 9.3
100 642 383 K 12 20:D1 C 23.6
101 642 383 K 13 21:D1 A 20.5
102 643 384 R 11 19:D1 G 12.4
103 643 384 R 12 20:D1 C 24.0
104 643 384 R 13 21:D1 A 25.5 H-bond
105 643 384 R 25 9:B1 G 2.2
106 643 384 R 26 10:B1 C 6.0
107 643 384 R 27 11:B1 G 37.0 H-bond
108 643 384 R 28 12:B1 T 11.2
109 644 385 K 13 21:D1 A 23.2
110 644 385 K 14 22:D1 T 25.3 H-bond
111 646 387 V 13 21:D1 A <0.1
112 720 461 E 29 13:B1 C 7.8
113 720 461 E 30 1:C1 G 0.7
114 737 478 K 2 10:D1 T 3.7
115 738 479 R 1 9:D1 G 20.8
116 738 479 R 2 10:D1 T 25.0 H-bond
117 739 480 S 2 10:D1 T 1.6
118 739 480 S 3 11:D1 C 14.1
119 740 481 H 2 10:D1 T 14.5
120 740 481 H 3 11:D1 C 0.7
121 744 485 K 30 1:C1 G 2.5
122 744 485 K 31 2:C1 T 16.9 H-bond
123 746 487 K 30 1:C1 G 5.5
124 746 487 K 31 2:C1 T 10.6 H-bond
125 748 489 D 31 2:C1 T 2.0
126 748 489 D 32 3:C1 C <0.1
127 749 490 Y 31 2:C1 T 20.8 H-bond
128 749 490 Y 32 3:C1 C 6.5
129 765 506 Y 8 16:D1 G 3.6
130 766 507 L 7 15:D1 C 2.7
131 767 508 G 7 15:D1 C 3.6
132 768 509 R 6 14:D1 A 9.2 H-bond
133 768 509 R 7 15:D1 C 20.5 H-bond
134 769 510 G 6 14:D1 A 9.3
135 770 511 K 4 12:D1 C 4.1
136 770 511 K 5 13:D1 G 32.7 H-bond
137 770 511 K 6 14:D1 A 34.0 H-bond
138 770 511 K 33 4:C1 G 10.2
139 770 511 K 34 5:C1 G <0.1
140 771 512 R 5 13:D1 G 1.0
141 771 512 R 6 14:D1 A 31.7
142 771 512 R 7 15:D1 C 3.6
143 771 512 R 33 4:C1 G 3.3
144 776 517 G 6 14:D1 A <0.1
145 776 517 G 7 15:D1 C 19.6
146 777 518 G 7 15:D1 C 6.9
147 777 518 G 8 16:D1 G 4.0
148 778 519 F 8 16:D1 G <0.1
149 794 535 C 8 16:D1 G 0.4
150 794 535 C 9 17:D1 A 8.5
151 795 536 K 8 16:D1 G 43.6 H-bond
152 795 536 K 9 17:D1 A 21.1 H-bond
153 796 537 L 7 15:D1 C 0.3
154 796 537 L 8 16:D1 G 8.0
155 797 538 G 6 14:D1 A 4.7
156 797 538 G 7 15:D1 C 22.8
157 797 538 G 8 16:D1 G 8.3
158 798 539 T 6 14:D1 A 8.4
159 798 539 T 7 15:D1 C 7.4
160 798 539 T 8 16:D1 G 2.9
161 798 539 T 30 1:C1 G 5.0
162 798 539 T 31 2:C1 T 17.6
163 798 539 T 32 3:C1 C 17.2
164 799 540 G 32 3:C1 C 16.6
165 799 540 G 33 4:C1 G 17.8
166 800 541 F 33 4:C1 G 12.0
167 801 542 S 33 4:C1 G 17.1
168 801 542 S 34 5:C1 G 11.2
169 802 543 D 33 4:C1 G 4.0
170 802 543 D 34 5:C1 G 37.7 H-bond
171 802 543 D 35 6:C1 A 0.2
172 803 544 E 34 5:C1 G 1.7
173 804 545 E 33 4:C1 G 0.4
174 845 586 K 32 3:C1 C 0.7
175 850 591 S 9 17:D1 A 6.2
176 850 591 S 10 18:D1 C 17.4 H-bond
177 851 592 L 10 18:D1 C 6.3
178 851 592 L 11 19:D1 G 2.7
179 852 593 S 10 18:D1 C 14.9 H-bond
180 853 594 P 10 18:D1 C 17.1
181 853 594 P 11 19:D1 G 20.0
182 854 595 I 10 18:D1 C 4.0
183 855 596 Y 9 17:D1 A 19.8 H-bond
184 855 596 Y 10 18:D1 C 5.9
185 866 607 K 11 19:D1 G 13.5
186 869 610 S 9 17:D1 A 12.5
187 869 610 S 10 18:D1 C 6.3
188 870 611 L 9 17:D1 A 12.8
189 871 612 R 8 16:D1 G 2.9
190 871 612 R 9 17:D1 A 6.5
191 871 612 R 29 13:B1 C 14.7
192 872 613 F 8 16:D1 G 21.0
193 872 613 F 9 17:D1 A 1.5
194 872 613 F 29 13:B1 C 14.9
195 872 613 F 30 1:C1 G 30.0
196 872 613 F 31 2:C1 T 20.1
197 873 614 P 8 16:D1 G 23.0
198 873 614 P 9 17:D1 A 5.1
199 873 614 P 31 2:C1 T 0.8
200 874 615 R 31 2:C1 T 21.8
201 874 615 R 32 3:C1 C 25.6 H-bond
202 875 616 F 32 3:C1 C 0.1
203 876 617 I 32 3:C1 C 4.6

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
B6p0d_D_B_C101AMP 48.0300.5

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

    Result domain: 6p0d_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: 67% (71/106).

    Identities = 41% (29/71), Positive = 55% (39/71), Gaps = 6% (4/71).

    Query: 480 PVQPMLAEACKSVEYAMKKCPNGMFS-EIKYDGERVQVHK-NGDHFSYFSRSLKPVLPHK 537

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

    6p0d_A: 280 PLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQA----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+

    6p0d_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+ + +

    6p0d_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 +

    6p0d_A: 456 VKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLD--GVGDTLDLVVIGAYLGRGKRA 513

    dssp: HH----EEEEEE---------------EEEEEHHH-- ----EEEEEEEEEEE--HHH-


    Query: 706 GMMSIFLMGCYDPGSQKWCTVTKCAGGHDDATLARLQNELDMVKISKDPSKIPSWLKVNK 765

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

    6p0d_A: 514 GRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVL---PSPRP-YVRIDG 569

    dssp: --EEEEEEEEEE----EEEEEEEE-----HHHHHHHHHHHH--EE ----- -EE---


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

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

    6p0d_A: 570 AVIPDHWL-DP--SAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPE 626

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


    Query: 818 SATNLPQLKELYQ 830

    AT Q+ LY+

    6p0d_A: 627 QATTSAQVACLYR 639

    dssp: H--EHHHHHHHHH


    Download alignment FASTA file