Interaction between DNA ligase 1 (6p0c_A) and DNA (6p0c_D_B_C)

PDB and SCOP data

PDB ID: 6p0c (all binary interactions in this PDB entry)

Title: Human DNA Ligase 1 Bound to an Adenylated, hydroxyl terminated DNA nick in EDTA

Release date: 2019-12-11

Resolution: 1.6 Å

  • Chain A: 6p0c_A

    Title: DNA ligase 1

    Source organism: Homo sapiens

    Number of residues: 645 (3 missing in structure)

  • Chain B: 6p0c_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: 2406.04 Å2

Number of inter-residue contacts at the interface: 202

Number of H-bonds: 37

  • 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 6p0c_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 303 44 S 42.6 40.8 %
    2 304 45 A 26.2 47.2 %
    3 305 46 R 85.6 58.8 %
    4 306 47 L 2.9 1.9 %
    5 345 86 L 4.2 6.9 %
    6 346 87 E 48.0 37.8 %
    7 347 88 L 11.0 34.9 %
    8 348 89 G 28.9 57.4 %
    9 349 90 V 18.0 96.7 %
    10 350 91 G 29.4 77.0 %
    11 351 92 D 5.1 11.6 %
    12 352 93 G 23.0 51.0 %
    13 353 94 V 21.4 55.8 %
    14 356 97 K 14.7 14.5 %
    15 370 111 R 3.8 3.8 %
    16 414 155 L 1.3 2.9 %
    17 415 156 T 14.4 12.1 %
    18 416 157 G 28.5 55.3 %
    19 417 158 S 14.2 12.4 %
    20 418 159 A 18.0 24.8 %
    21 419 160 S 16.3 94.7 %
    22 420 161 T 37.0 58.1 %
    23 421 162 A 1.5 2.4 %
    24 423 164 K 3.9 21.3 %
    25 446 187 L <0.1 0.0 %
    26 449 190 R 36.5 32.5 %
    27 450 191 L 0.2 1.2 %
    28 451 192 R 34.2 37.6 %
    29 452 193 L 7.7 60.3 %
    30 453 194 G 35.4 65.5 %
    31 454 195 L 14.3 74.7 %
    32 455 196 A 39.6 59.7 %
    33 456 197 E 4.6 11.4 %
    34 457 198 Q 53.0 53.4 %
    35 458 199 S 15.3 79.7 %
    36 504 245 K 12.3 22.4 %
    37 546 287 H 34.9 57.3 %
    38 547 288 P 6.1 9.7 %
    39 549 290 R 28.1 21.5 %
    40 557 298 R 25.0 29.7 %
    41 568 309 K 9.4 97.1 %
    42 570 311 D 3.1 15.1 %
    43 571 312 G 12.5 99.8 %
    44 572 313 Q 32.2 73.0 %
    45 573 314 R 12.8 87.2 %
    46 588 329 S 20.7 91.3 %
    47 589 330 R 43.7 47.4 %
    48 590 331 N 30.0 30.7 %
    49 592 333 E 40.8 55.0 %
    50 594 335 N 2.9 11.3 %
    51 621 362 E 3.9 87.1 %
    52 635 376 F 40.2 67.3 %
    53 636 377 Q 34.3 45.9 %
    54 639 380 T 41.8 59.4 %
    55 640 381 T 35.1 38.8 %
    56 641 382 R 9.1 47.2 %
    57 642 383 K 44.3 28.5 %
    58 643 384 R 97.1 58.2 %
    59 644 385 K 50.9 31.7 %
    60 720 461 E 8.9 26.8 %
    61 737 478 K 3.5 2.4 %
    62 738 479 R 41.7 34.2 %
    63 739 480 S 16.1 39.5 %
    64 740 481 H 7.0 11.7 %
    65 744 485 K 19.1 66.0 %
    66 746 487 K 17.0 85.5 %
    67 748 489 D 1.7 11.0 %
    68 749 490 Y 27.4 94.6 %
    69 765 506 Y 3.8 13.6 %
    70 766 507 L 2.4 4.8 %
    71 767 508 G 3.7 83.9 %
    72 768 509 R 30.9 35.2 %
    73 769 510 G 11.2 65.9 %
    74 770 511 K 84.6 46.2 %
    75 771 512 R 37.3 57.4 %
    76 776 517 G 19.3 98.1 %
    77 777 518 G 11.1 87.1 %
    78 778 519 F <0.1 85.1 %
    79 794 535 C 9.1 100.0 %
    80 795 536 K 62.2 70.3 %
    81 796 537 L 8.4 100.0 %
    82 797 538 G 35.7 99.6 %
    83 798 539 T 58.8 91.9 %
    84 799 540 G 34.2 88.2 %
    85 800 541 F 12.2 91.3 %
    86 801 542 S 28.1 51.0 %
    87 802 543 D 42.0 40.3 %
    88 803 544 E 1.6 1.3 %
    89 804 545 E 0.5 0.9 %
    90 845 586 K 1.0 9.0 %
    91 850 591 S 23.2 71.1 %
    92 851 592 L 8.7 21.9 %
    93 852 593 S 14.0 98.8 %
    94 853 594 P 40.8 37.7 %
    95 854 595 I 9.2 12.1 %
    96 855 596 Y 23.6 96.1 %
    97 866 607 K 8.6 10.1 %
    98 869 610 S 19.3 100.0 %
    99 870 611 L 13.0 100.0 %
    100 871 612 R 24.2 48.9 %
    101 872 613 F 87.0 96.0 %
    102 873 614 P 29.0 94.3 %
    103 874 615 R 47.5 99.8 %
    104 875 616 F 0.2 5.4 %
    105 876 617 I 4.8 6.6 %

  • Interface residues in 6p0c_D_B_C

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 9:D1 G 50.7 21.9 %
    2 2 10:D1 T 83.3 49.9 %
    3 3 11:D1 C 106.8 58.9 %
    4 4 12:D1 C 93.7 63.0 %
    5 5 13:D1 G 91.5 50.3 %
    6 6 14:D1 A 145.2 88.4 %
    7 7 15:D1 C 104.3 64.4 %
    8 8 16:D1 G 115.3 63.9 %
    9 9 17:D1 A 100.1 70.6 %
    10 10 18:D1 C 88.8 59.3 %
    11 11 19:D1 G 102.7 62.1 %
    12 12 20:D1 C 95.1 55.9 %
    13 13 21:D1 A 84.0 56.8 %
    14 14 22:D1 T 17.3 8.9 %
    15 15 23:D1 C 76.5 44.7 %
    16 16 24:D1 A 58.8 41.2 %
    17 17 25:D1 G 14.5 8.1 %
    18 24 8:B1 T 21.8 10.7 %
    19 25 9:B1 G 91.9 57.6 %
    20 26 10:B1 C 71.6 43.7 %
    21 27 11:B1 G 67.1 37.5 %
    22 28 12:B1 T 99.6 62.8 %
    23 29 13:B1 C 128.4 84.5 %
    24 30 1:C1 G 74.7 75.3 %
    25 31 2:C1 T 112.3 76.7 %
    26 32 3:C1 C 103.7 65.9 %
    27 33 4:C1 G 63.1 32.9 %
    28 34 5:C1 G 50.8 30.0 %
    29 35 6:C1 A 30.3 16.6 %
    30 36 7:C1 C 61.9 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 21.0
2 303 44 S 36 7:C1 C 21.6 H-bond
3 304 45 A 36 7:C1 C 26.2
4 305 46 R 1 9:D1 G 4.1
5 305 46 R 2 10:D1 T 16.7 H-bond
6 305 46 R 3 11:D1 C 37.3
7 305 46 R 4 12:D1 C 8.0
8 305 46 R 34 5:C1 G <0.1
9 305 46 R 35 6:C1 A 8.3
10 305 46 R 36 7:C1 C 11.2
11 306 47 L 36 7:C1 C 2.9
12 345 86 L 27 11:B1 G 4.2
13 346 87 E 26 10:B1 C 31.7
14 346 87 E 27 11:B1 G 16.3
15 347 88 L 26 10:B1 C 11.0
16 348 89 G 25 9:B1 G 20.6
17 348 89 G 26 10:B1 C 8.3 H-bond
18 349 90 V 25 9:B1 G 4.7
19 349 90 V 26 10:B1 C 13.3
20 350 91 G 25 9:B1 G 24.6 H-bond
21 350 91 G 26 10:B1 C 4.8
22 351 92 D 25 9:B1 G 5.1
23 352 93 G 24 8:B1 T 10.8
24 352 93 G 25 9:B1 G 12.2
25 353 94 V 24 8:B1 T 7.2
26 353 94 V 25 9:B1 G 14.2 H-bond
27 356 97 K 16 24:D1 A 0.2
28 356 97 K 17 25:D1 G 14.5
29 370 111 R 24 8:B1 T 3.8
30 414 155 L 15 23:D1 C 1.3
31 415 156 T 15 23:D1 C 14.4
32 416 157 G 15 23:D1 C 28.2 H-bond
33 416 157 G 16 24:D1 A 0.3
34 417 158 S 15 23:D1 C 6.4
35 417 158 S 16 24:D1 A 7.8
36 418 159 A 16 24:D1 A 18.0 H-bond
37 419 160 S 15 23:D1 C 12.5
38 419 160 S 16 24:D1 A 3.8
39 420 161 T 15 23:D1 C 9.8
40 420 161 T 16 24:D1 A 27.2 H-bond
41 421 162 A 16 24:D1 A 1.5
42 423 164 K 15 23:D1 C 3.9
43 446 187 L 26 10:B1 C <0.1
44 449 190 R 6 14:D1 A 20.8
45 449 190 R 7 15:D1 C 15.7 H-bond
46 450 191 L 5 13:D1 G 0.2
47 451 192 R 5 13:D1 G 11.4
48 451 192 R 6 14:D1 A 22.8
49 452 193 L 5 13:D1 G 7.7
50 453 194 G 4 12:D1 C 19.1
51 453 194 G 5 13:D1 G 16.3 H-bond
52 454 195 L 4 12:D1 C 5.6
53 454 195 L 5 13:D1 G 8.7
54 455 196 A 4 12:D1 C 26.2 H-bond
55 455 196 A 5 13:D1 G 13.4
56 456 197 E 4 12:D1 C 4.6
57 457 198 Q 3 11:D1 C 39.1
58 457 198 Q 4 12:D1 C 14.0 H-bond
59 458 199 S 3 11:D1 C 3.0
60 458 199 S 4 12:D1 C 12.2 H-bond
61 504 245 K 3 11:D1 C 12.3
62 546 287 H 1 9:D1 G 6.4
63 546 287 H 2 10:D1 T 27.7 H-bond
64 546 287 H 3 11:D1 C 0.8
65 547 288 P 31 2:C1 T 2.1
66 547 288 P 32 3:C1 C 4.0
67 549 290 R 32 3:C1 C 28.1 H-bond
68 557 298 R 1 9:D1 G 23.1
69 557 298 R 2 10:D1 T 1.9
70 568 309 K 29 13:B1 C <0.1
71 568 309 K 30 1:C1 G 9.3 H-bond
72 570 311 D 29 13:B1 C 3.1
73 571 312 G 29 13:B1 C 12.5
74 572 313 Q 28 12:B1 T 21.5
75 572 313 Q 29 13:B1 C 10.7
76 573 314 R 29 13:B1 C 12.8 H-bond
77 588 329 S 28 12:B1 T 19.6 H-bond
78 588 329 S 29 13:B1 C 1.0
79 589 330 R 28 12:B1 T 0.6
80 589 330 R 29 13:B1 C 22.5
81 589 330 R 30 1:C1 G 20.6
82 590 331 N 28 12:B1 T 25.1 H-bond
83 590 331 N 29 13:B1 C 4.8
84 592 333 E 27 11:B1 G 33.3
85 592 333 E 28 12:B1 T 7.5
86 594 335 N 28 12:B1 T 2.9
87 621 362 E 29 13:B1 C 3.7
88 621 362 E 30 1:C1 G 0.2
89 635 376 F 9 17:D1 A 4.5
90 635 376 F 28 12:B1 T 17.3
91 635 376 F 29 13:B1 C 18.4
92 636 377 Q 10 18:D1 C 11.9
93 636 377 Q 11 19:D1 G 22.5 H-bond
94 639 380 T 11 19:D1 G 28.7
95 639 380 T 12 20:D1 C 7.6
96 639 380 T 27 11:B1 G 0.4
97 639 380 T 28 12:B1 T 5.1
98 640 381 T 11 19:D1 G 11.6
99 640 381 T 12 20:D1 C 23.5
100 641 382 R 12 20:D1 C 9.1
101 642 383 K 12 20:D1 C 23.7
102 642 383 K 13 21:D1 A 20.6
103 643 384 R 11 19:D1 G 10.1
104 643 384 R 12 20:D1 C 31.1
105 643 384 R 13 21:D1 A 29.8 H-bond
106 643 384 R 25 9:B1 G 10.5
107 643 384 R 26 10:B1 C 2.6
108 643 384 R 27 11:B1 G 13.0
109 644 385 K 13 21:D1 A 33.6
110 644 385 K 14 22:D1 T 17.3
111 720 461 E 29 13:B1 C 7.6
112 720 461 E 30 1:C1 G 1.3
113 737 478 K 2 10:D1 T 3.5
114 738 479 R 1 9:D1 G 17.1
115 738 479 R 2 10:D1 T 24.6 H-bond
116 739 480 S 2 10:D1 T 1.9
117 739 480 S 3 11:D1 C 14.2
118 740 481 H 2 10:D1 T 7.0
119 744 485 K 30 1:C1 G 1.9
120 744 485 K 31 2:C1 T 17.1 H-bond
121 746 487 K 30 1:C1 G 6.3
122 746 487 K 31 2:C1 T 10.7 H-bond
123 748 489 D 31 2:C1 T 1.7
124 748 489 D 32 3:C1 C <0.1
125 749 490 Y 31 2:C1 T 20.7 H-bond
126 749 490 Y 32 3:C1 C 6.7
127 765 506 Y 8 16:D1 G 3.8
128 766 507 L 7 15:D1 C 2.4
129 767 508 G 7 15:D1 C 3.7
130 768 509 R 6 14:D1 A 9.2 H-bond
131 768 509 R 7 15:D1 C 21.7 H-bond
132 769 510 G 6 14:D1 A 11.2
133 770 511 K 4 12:D1 C 4.0
134 770 511 K 5 13:D1 G 33.4 H-bond
135 770 511 K 6 14:D1 A 36.8 H-bond
136 770 511 K 33 4:C1 G 10.3
137 770 511 K 34 5:C1 G 0.2
138 771 512 R 5 13:D1 G 0.5
139 771 512 R 6 14:D1 A 31.1
140 771 512 R 7 15:D1 C 3.7
141 771 512 R 33 4:C1 G 2.0
142 776 517 G 6 14:D1 A <0.1
143 776 517 G 7 15:D1 C 19.3
144 777 518 G 7 15:D1 C 6.8
145 777 518 G 8 16:D1 G 4.3
146 778 519 F 8 16:D1 G <0.1
147 794 535 C 8 16:D1 G 0.3
148 794 535 C 9 17:D1 A 8.8
149 795 536 K 8 16:D1 G 41.7 H-bond
150 795 536 K 9 17:D1 A 20.6 H-bond
151 796 537 L 7 15:D1 C 0.3
152 796 537 L 8 16:D1 G 8.1
153 797 538 G 6 14:D1 A 4.9
154 797 538 G 7 15:D1 C 22.9
155 797 538 G 8 16:D1 G 8.0
156 798 539 T 6 14:D1 A 8.5
157 798 539 T 7 15:D1 C 7.8
158 798 539 T 8 16:D1 G 2.8
159 798 539 T 30 1:C1 G 5.1
160 798 539 T 31 2:C1 T 17.7 H-bond
161 798 539 T 32 3:C1 C 16.9
162 799 540 G 32 3:C1 C 16.4
163 799 540 G 33 4:C1 G 17.8
164 800 541 F 33 4:C1 G 12.2
165 801 542 S 33 4:C1 G 17.0
166 801 542 S 34 5:C1 G 11.1
167 802 543 D 33 4:C1 G 3.3
168 802 543 D 34 5:C1 G 37.7 H-bond
169 802 543 D 35 6:C1 A 1.0
170 803 544 E 34 5:C1 G 1.6
171 804 545 E 33 4:C1 G 0.5
172 845 586 K 32 3:C1 C 1.0
173 850 591 S 9 17:D1 A 6.0
174 850 591 S 10 18:D1 C 17.3 H-bond
175 851 592 L 10 18:D1 C 6.0
176 851 592 L 11 19:D1 G 2.7
177 852 593 S 10 18:D1 C 14.0 H-bond
178 853 594 P 10 18:D1 C 22.2
179 853 594 P 11 19:D1 G 18.5
180 854 595 I 9 17:D1 A 2.9
181 854 595 I 10 18:D1 C 6.3
182 855 596 Y 9 17:D1 A 19.4 H-bond
183 855 596 Y 10 18:D1 C 4.2
184 866 607 K 11 19:D1 G 8.6
185 869 610 S 9 17:D1 A 12.5
186 869 610 S 10 18:D1 C 6.9
187 870 611 L 9 17:D1 A 13.0
188 871 612 R 8 16:D1 G 2.9
189 871 612 R 9 17:D1 A 5.8
190 871 612 R 29 13:B1 C 15.5
191 872 613 F 8 16:D1 G 20.4
192 872 613 F 9 17:D1 A 1.4
193 872 613 F 29 13:B1 C 15.6
194 872 613 F 30 1:C1 G 29.9
195 872 613 F 31 2:C1 T 19.6
196 873 614 P 8 16:D1 G 23.0
197 873 614 P 9 17:D1 A 5.2
198 873 614 P 31 2:C1 T 0.7
199 874 615 R 31 2:C1 T 22.0
200 874 615 R 32 3:C1 C 25.5 H-bond
201 875 616 F 32 3:C1 C 0.2
202 876 617 I 32 3:C1 C 4.8

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
B6p0c_D_B_C101AMP 47.0304.7

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

    Result domain: 6p0c_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: 66% (69/105).

    Identities = 42% (29/69), Positive = 58% (40/69), Gaps = 4% (3/69).

    Query: 480 PVQPMLAEACKSVEYAMKKCPNGMFS-EIKYDGERVQVHK-NGDHFSYFSRSLKPVLPHK 537

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

    6p0c_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+

    6p0c_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+ + +

    6p0c_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 +

    6p0c_A: 456 VKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLD--GVGDTLDLVVIGAYLGRGKRA 513

    dssp: HH-----EEEEE---------------EEEE-HHH-- ----EEEEEEEEEEE--HHH-


    Query: 706 GMMSIFLMGCYDPGSQKWCTVTKCAGGHDDATLARLQNELDMVKISKDPSKIPSWLKVNK 765

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

    6p0c_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 +

    6p0c_A: 570 AVIPDHWL-DP--SAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPE 626

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


    Query: 818 SATNLPQLKELYQ 830

    AT Q+ LY+

    6p0c_A: 627 QATTSAQVACLYR 639

    dssp: H--EHHHHHHHHH


    Download alignment FASTA file