Interaction between DNA ligase 1 (6p0e_A) and DNA (6p0e_D_B_C)

PDB and SCOP data

PDB ID: 6p0e (all binary interactions in this PDB entry)

Title: Human DNA Ligase 1 (E346A,E592A) bound to adenylated DNA containing an 8-oxo guanine:adenine base-pair

Release date: 2019-12-11

Resolution: 1.9 Å

  • Chain A: 6p0e_A

    Title: DNA ligase 1

    Source organism: Homo sapiens

    Number of residues: 645 (3 missing in structure)

  • Chain B: 6p0e_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: 2409.63 Å2

Number of inter-residue contacts at the interface: 195

Number of H-bonds: 39

  • 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 6p0e_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 303 44 S 42.9 39.0 %
    2 304 45 A 25.5 45.2 %
    3 305 46 R 51.4 44.9 %
    4 306 47 L 4.8 3.6 %
    5 344 85 G 13.7 22.9 %
    6 345 86 L 4.4 7.6 %
    7 346 87 A 34.0 57.0 %
    8 347 88 L 9.2 32.4 %
    9 348 89 G 32.0 57.1 %
    10 349 90 V 20.5 88.6 %
    11 350 91 G 26.8 74.2 %
    12 351 92 D 5.1 11.4 %
    13 352 93 G 26.6 55.9 %
    14 353 94 V 22.4 61.1 %
    15 356 97 K 12.6 13.3 %
    16 370 111 R 10.0 10.0 %
    17 414 155 L 0.4 1.0 %
    18 415 156 T 14.7 12.3 %
    19 416 157 G 27.2 52.0 %
    20 417 158 S 16.4 14.2 %
    21 418 159 A 18.2 25.8 %
    22 419 160 S 16.4 96.7 %
    23 420 161 T 37.7 60.3 %
    24 421 162 A 1.3 2.1 %
    25 423 164 K 0.6 4.5 %
    26 449 190 R 36.4 33.7 %
    27 451 192 R 46.6 47.4 %
    28 452 193 L 5.7 48.8 %
    29 453 194 G 35.0 64.2 %
    30 454 195 L 13.8 75.6 %
    31 455 196 A 39.6 60.4 %
    32 456 197 E 4.6 10.8 %
    33 457 198 Q 51.5 55.6 %
    34 458 199 S 11.9 100.0 %
    35 504 245 K 12.2 22.7 %
    36 544 285 L <0.1 0.0 %
    37 546 287 H 25.6 38.7 %
    38 547 288 P 7.5 14.4 %
    39 549 290 R 26.7 19.8 %
    40 557 298 R 32.4 37.7 %
    41 568 309 K 9.6 92.5 %
    42 570 311 D 2.1 10.1 %
    43 571 312 G 11.0 96.4 %
    44 572 313 Q 40.3 82.6 %
    45 573 314 R 13.1 89.3 %
    46 588 329 S 21.7 91.8 %
    47 589 330 R 59.7 59.9 %
    48 590 331 N 40.7 40.0 %
    49 592 333 A 16.2 39.4 %
    50 594 335 N 3.2 12.4 %
    51 597 338 K 0.7 3.6 %
    52 621 362 E 2.5 67.7 %
    53 635 376 F 37.5 66.8 %
    54 636 377 Q 32.4 42.8 %
    55 639 380 T 41.4 64.7 %
    56 640 381 T 38.4 42.4 %
    57 641 382 R 9.1 56.9 %
    58 642 383 K 42.8 28.3 %
    59 643 384 R 100.6 64.4 %
    60 644 385 K 54.9 31.2 %
    61 720 461 E 8.4 26.0 %
    62 737 478 K 4.7 3.2 %
    63 738 479 R 43.9 36.4 %
    64 739 480 S 16.8 41.2 %
    65 740 481 H 13.4 18.1 %
    66 744 485 K 19.3 69.1 %
    67 746 487 K 20.2 86.7 %
    68 748 489 D 2.3 15.6 %
    69 749 490 Y 26.5 86.5 %
    70 765 506 Y 3.3 12.9 %
    71 766 507 L 2.6 5.0 %
    72 767 508 G 3.9 85.7 %
    73 768 509 R 30.4 35.8 %
    74 769 510 G 9.4 53.0 %
    75 770 511 K 82.5 47.7 %
    76 771 512 R 38.7 59.1 %
    77 776 517 G 19.2 98.2 %
    78 777 518 G 11.1 88.3 %
    79 778 519 F <0.1 9.9 %
    80 794 535 C 9.0 100.0 %
    81 795 536 K 64.4 70.3 %
    82 796 537 L 7.9 100.0 %
    83 797 538 G 35.1 99.8 %
    84 798 539 T 58.9 92.9 %
    85 799 540 G 34.9 88.3 %
    86 800 541 F 12.3 92.3 %
    87 801 542 S 28.4 51.8 %
    88 802 543 D 41.9 40.4 %
    89 803 544 E 1.7 1.3 %
    90 804 545 E 0.7 1.3 %
    91 845 586 K 0.4 2.7 %
    92 847 588 A <0.1 0.2 %
    93 850 591 S 22.8 71.7 %
    94 851 592 L 7.7 19.3 %
    95 852 593 S 13.7 97.4 %
    96 853 594 P 40.9 39.3 %
    97 854 595 I 7.9 13.6 %
    98 855 596 Y 24.3 96.1 %
    99 866 607 K 12.1 14.1 %
    100 869 610 S 19.0 100.0 %
    101 870 611 L 12.6 100.0 %
    102 871 612 R 21.9 46.5 %
    103 872 613 F 90.8 95.3 %
    104 873 614 P 27.9 95.9 %
    105 874 615 R 48.1 99.6 %
    106 875 616 F 0.2 3.5 %
    107 876 617 I 5.2 7.1 %

  • Interface residues in 6p0e_D_B_C

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 9:D1 G 51.8 22.6 %
    2 2 10:D1 T 69.8 41.9 %
    3 3 11:D1 C 101.5 59.7 %
    4 4 12:D1 C 93.7 63.4 %
    5 5 13:D1 G 97.7 52.4 %
    6 6 14:D1 A 142.6 88.6 %
    7 7 15:D1 C 105.6 66.2 %
    8 8 16:D1 A 113.0 67.0 %
    9 9 17:D1 A 101.9 74.1 %
    10 10 18:D1 C 89.1 72.4 %
    11 11 19:D1 G 113.4 72.7 %
    12 12 20:D1 C 88.1 53.3 %
    13 13 21:D1 A 80.9 55.3 %
    14 14 22:D1 T 19.9 10.4 %
    15 15 23:D1 C 72.7 43.6 %
    16 16 24:D1 A 61.4 41.5 %
    17 17 25:D1 G 11.4 6.3 %
    18 24 8:B1 T 32.0 17.0 %
    19 25 9:B1 G 88.6 60.3 %
    20 26 10:B1 C 69.9 50.2 %
    21 27 11:B1 G 55.2 36.8 %
    22 28 12:B1 T 105.8 66.5 %
    23 29 13:B1 8OG 150.4 86.8 %
    24 30 1:C1 G 81.1 69.1 %
    25 31 2:C1 T 114.8 75.8 %
    26 32 3:C1 C 101.7 64.0 %
    27 33 4:C1 G 64.4 33.7 %
    28 34 5:C1 G 51.3 30.3 %
    29 35 6:C1 A 23.4 13.1 %
    30 36 7:C1 C 56.5 20.2 %

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 22.9
2 303 44 S 36 7:C1 C 20.1 H-bond
3 304 45 A 36 7:C1 C 25.5
4 305 46 R 2 10:D1 T 0.5
5 305 46 R 3 11:D1 C 35.9
6 305 46 R 4 12:D1 C 8.9
7 305 46 R 36 7:C1 C 6.1
8 306 47 L 36 7:C1 C 4.8
9 344 85 G 27 11:B1 G 13.7
10 345 86 L 27 11:B1 G 4.4
11 346 87 A 26 10:B1 C 21.8
12 346 87 A 27 11:B1 G 12.2
13 347 88 L 26 10:B1 C 9.2
14 348 89 G 25 9:B1 G 18.9
15 348 89 G 26 10:B1 C 13.1 H-bond
16 349 90 V 25 9:B1 G 7.0
17 349 90 V 26 10:B1 C 13.4
18 350 91 G 25 9:B1 G 23.1 H-bond
19 350 91 G 26 10:B1 C 3.7
20 351 92 D 25 9:B1 G 5.1
21 352 93 G 24 8:B1 T 14.6
22 352 93 G 25 9:B1 G 12.0 H-bond
23 353 94 V 24 8:B1 T 7.4
24 353 94 V 25 9:B1 G 15.0 H-bond
25 356 97 K 16 24:D1 A 1.2
26 356 97 K 17 25:D1 G 11.4
27 370 111 R 24 8:B1 T 10.0
28 414 155 L 15 23:D1 C 0.4
29 415 156 T 15 23:D1 C 14.7
30 416 157 G 15 23:D1 C 26.8 H-bond
31 416 157 G 16 24:D1 A 0.4
32 417 158 S 15 23:D1 C 7.7
33 417 158 S 16 24:D1 A 8.7
34 418 159 A 16 24:D1 A 18.2 H-bond
35 419 160 S 15 23:D1 C 12.3
36 419 160 S 16 24:D1 A 4.1
37 420 161 T 15 23:D1 C 10.1
38 420 161 T 16 24:D1 A 27.5 H-bond
39 421 162 A 16 24:D1 A 1.3
40 423 164 K 15 23:D1 C 0.6
41 449 190 R 6 14:D1 A 19.2
42 449 190 R 7 15:D1 C 17.2 H-bond
43 451 192 R 5 13:D1 G 20.0
44 451 192 R 6 14:D1 A 26.6 H-bond
45 452 193 L 5 13:D1 G 5.7
46 453 194 G 4 12:D1 C 18.8
47 453 194 G 5 13:D1 G 16.2 H-bond
48 454 195 L 4 12:D1 C 5.5
49 454 195 L 5 13:D1 G 8.3
50 455 196 A 4 12:D1 C 26.2 H-bond
51 455 196 A 5 13:D1 G 13.4
52 456 197 E 4 12:D1 C 4.6
53 457 198 Q 3 11:D1 C 37.3
54 457 198 Q 4 12:D1 C 14.2 H-bond
55 458 199 S 3 11:D1 C 0.7
56 458 199 S 4 12:D1 C 11.3 H-bond
57 504 245 K 3 11:D1 C 12.2
58 544 285 L 30 1:C1 G <0.1
59 546 287 H 1 9:D1 G 6.4
60 546 287 H 2 10:D1 T 19.2
61 547 288 P 31 2:C1 T 3.1
62 547 288 P 32 3:C1 C 4.4
63 549 290 R 32 3:C1 C 26.7 H-bond
64 557 298 R 1 9:D1 G 27.7
65 557 298 R 2 10:D1 T 4.7
66 568 309 K 29 13:B1 8OG 0.2
67 568 309 K 30 1:C1 G 9.4 H-bond
68 570 311 D 29 13:B1 8OG 2.1
69 571 312 G 29 13:B1 8OG 11.0
70 572 313 Q 28 12:B1 T 28.2
71 572 313 Q 29 13:B1 8OG 12.1
72 573 314 R 29 13:B1 8OG 13.1 H-bond
73 588 329 S 28 12:B1 T 20.4 H-bond
74 588 329 S 29 13:B1 8OG 1.3
75 589 330 R 29 13:B1 8OG 36.4
76 589 330 R 30 1:C1 G 23.3 H-bond
77 590 331 N 28 12:B1 T 28.8 H-bond
78 590 331 N 29 13:B1 8OG 12.0
79 592 333 A 27 11:B1 G 7.1
80 592 333 A 28 12:B1 T 9.2
81 594 335 N 28 12:B1 T 3.2
82 597 338 K 28 12:B1 T 0.7
83 621 362 E 29 13:B1 8OG 2.5
84 635 376 F 9 17:D1 A 4.4
85 635 376 F 28 12:B1 T 12.7
86 635 376 F 29 13:B1 8OG 20.4
87 636 377 Q 10 18:D1 C 12.3
88 636 377 Q 11 19:D1 G 20.1 H-bond
89 639 380 T 11 19:D1 G 32.3 H-bond
90 639 380 T 12 20:D1 C 6.3
91 639 380 T 27 11:B1 G 0.1
92 639 380 T 28 12:B1 T 2.7
93 640 381 T 11 19:D1 G 17.3
94 640 381 T 12 20:D1 C 21.1
95 641 382 R 12 20:D1 C 9.1
96 642 383 K 12 20:D1 C 21.8
97 642 383 K 13 21:D1 A 21.0
98 643 384 R 11 19:D1 G 12.1
99 643 384 R 12 20:D1 C 29.7 H-bond
100 643 384 R 13 21:D1 A 24.8 H-bond
101 643 384 R 25 9:B1 G 7.5
102 643 384 R 26 10:B1 C 8.7
103 643 384 R 27 11:B1 G 17.7
104 644 385 K 13 21:D1 A 35.1
105 644 385 K 14 22:D1 T 19.9
106 720 461 E 29 13:B1 8OG 7.4
107 720 461 E 30 1:C1 G 1.0
108 737 478 K 2 10:D1 T 4.7
109 738 479 R 1 9:D1 G 17.8
110 738 479 R 2 10:D1 T 26.1 H-bond
111 739 480 S 2 10:D1 T 1.3
112 739 480 S 3 11:D1 C 15.5
113 740 481 H 2 10:D1 T 13.4
114 744 485 K 30 1:C1 G 2.5
115 744 485 K 31 2:C1 T 16.8 H-bond
116 746 487 K 30 1:C1 G 9.0
117 746 487 K 31 2:C1 T 11.1 H-bond
118 748 489 D 31 2:C1 T 2.3
119 749 490 Y 31 2:C1 T 20.7 H-bond
120 749 490 Y 32 3:C1 C 5.8
121 765 506 Y 8 16:D1 A 3.3
122 766 507 L 7 15:D1 C 2.6
123 767 508 G 7 15:D1 C 3.9
124 768 509 R 6 14:D1 A 9.0 H-bond
125 768 509 R 7 15:D1 C 21.4 H-bond
126 769 510 G 6 14:D1 A 9.4
127 770 511 K 4 12:D1 C 4.2
128 770 511 K 5 13:D1 G 33.0 H-bond
129 770 511 K 6 14:D1 A 34.4 H-bond
130 770 511 K 33 4:C1 G 10.6
131 770 511 K 34 5:C1 G 0.3
132 771 512 R 5 13:D1 G 1.1
133 771 512 R 6 14:D1 A 31.6
134 771 512 R 7 15:D1 C 3.3
135 771 512 R 33 4:C1 G 2.7
136 776 517 G 7 15:D1 C 19.2
137 777 518 G 7 15:D1 C 6.8
138 777 518 G 8 16:D1 A 4.3
139 778 519 F 8 16:D1 A <0.1
140 794 535 C 8 16:D1 A 0.4
141 794 535 C 9 17:D1 A 8.5
142 795 536 K 8 16:D1 A 44.1 H-bond
143 795 536 K 9 17:D1 A 20.3 H-bond
144 796 537 L 7 15:D1 C 0.2
145 796 537 L 8 16:D1 A 7.7
146 797 538 G 6 14:D1 A 4.3
147 797 538 G 7 15:D1 C 22.9
148 797 538 G 8 16:D1 A 7.9
149 798 539 T 6 14:D1 A 8.1
150 798 539 T 7 15:D1 C 8.0
151 798 539 T 8 16:D1 A 3.5
152 798 539 T 30 1:C1 G 5.1
153 798 539 T 31 2:C1 T 17.7 H-bond
154 798 539 T 32 3:C1 C 16.5
155 799 540 G 32 3:C1 C 17.3
156 799 540 G 33 4:C1 G 17.5
157 800 541 F 33 4:C1 G 12.3
158 801 542 S 33 4:C1 G 17.0
159 801 542 S 34 5:C1 G 11.4
160 802 543 D 33 4:C1 G 3.5
161 802 543 D 34 5:C1 G 37.9 H-bond
162 802 543 D 35 6:C1 A 0.5
163 803 544 E 34 5:C1 G 1.7
164 804 545 E 33 4:C1 G 0.7
165 845 586 K 32 3:C1 C 0.4
166 847 588 A 31 2:C1 T <0.1
167 850 591 S 9 17:D1 A 6.6
168 850 591 S 10 18:D1 C 16.2 H-bond
169 851 592 L 10 18:D1 C 5.6
170 851 592 L 11 19:D1 G 2.1
171 852 593 S 10 18:D1 C 13.7 H-bond
172 853 594 P 10 18:D1 C 23.6
173 853 594 P 11 19:D1 G 17.4
174 854 595 I 9 17:D1 A 1.9
175 854 595 I 10 18:D1 C 6.0
176 855 596 Y 9 17:D1 A 19.3 H-bond
177 855 596 Y 10 18:D1 C 5.0
178 866 607 K 11 19:D1 G 12.1
179 869 610 S 9 17:D1 A 12.3
180 869 610 S 10 18:D1 C 6.6
181 870 611 L 9 17:D1 A 12.6
182 871 612 R 9 17:D1 A 9.2
183 871 612 R 29 13:B1 8OG 12.7
184 872 613 F 8 16:D1 A 19.3
185 872 613 F 9 17:D1 A 2.4
186 872 613 F 29 13:B1 8OG 19.2
187 872 613 F 30 1:C1 G 30.8
188 872 613 F 31 2:C1 T 19.1
189 873 614 P 8 16:D1 A 22.5
190 873 614 P 9 17:D1 A 4.4
191 873 614 P 31 2:C1 T 1.0
192 874 615 R 31 2:C1 T 22.9
193 874 615 R 32 3:C1 C 25.2
194 875 616 F 32 3:C1 C 0.2
195 876 617 I 32 3:C1 C 5.2

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
B6p0e_D_B_C101TRS 107.015.9
B6p0e_D_B_C101TRS 81.35.2
B6p0e_D_B_C101AMP 47.3297.3

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

    Result domain: 6p0e_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% (72/107).

    Identities = 43% (31/72), Positive = 57% (41/72), Gaps = 4% (3/72).

    Query: 480 PVQPMLAEACKSVEYAMKKCPNGMFS-EIKYDGERVQVHK-NGDHFSYFSRSLKPVLPHK 537

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

    6p0e_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+

    6p0e_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+ + +

    6p0e_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 +

    6p0e_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 +++++

    6p0e_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 +

    6p0e_A: 570 AVIPDHWL-DP--SAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPE 626

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


    Query: 818 SATNLPQLKELYQ 830

    AT Q+ LY+

    6p0e_A: 627 QATTSAQVACLYR 639

    dssp: H--EHHHHHHHHH


    Download alignment FASTA file