Interaction between DNA ligase 1 (6p0a_A) and DNA (6p0a_D_B_C)

PDB and SCOP data

PDB ID: 6p0a (all binary interactions in this PDB entry)

Title: Human DNA Ligase 1 Bound to an Adenylated, dideoxy Terminated DNA nick with 2 mM Mg2+

Release date: 2019-12-11

Resolution: 2.0 Å

  • Chain A: 6p0a_A

    Title: DNA ligase 1

    Source organism: Homo sapiens

    Number of residues: 645 (6 missing in structure)

  • Chain B: 6p0a_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: 2267.01 Å2

Number of inter-residue contacts at the interface: 187

Number of H-bonds: 31

  • 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 6p0a_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 303 44 S 42.7 39.3 %
    2 304 45 A 25.6 44.2 %
    3 305 46 R 50.4 44.1 %
    4 306 47 L 0.9 0.6 %
    5 346 87 E 46.5 41.7 %
    6 347 88 L 11.6 36.9 %
    7 348 89 G 27.0 48.5 %
    8 349 90 V 20.1 88.0 %
    9 350 91 G 26.6 84.0 %
    10 351 92 D 5.3 11.9 %
    11 352 93 G 7.5 17.4 %
    12 353 94 V 3.1 10.6 %
    13 415 156 T 14.3 11.2 %
    14 416 157 G 25.7 53.3 %
    15 417 158 S 16.1 13.1 %
    16 418 159 A 16.5 23.1 %
    17 419 160 S 15.7 90.0 %
    18 420 161 T 38.5 68.4 %
    19 421 162 A 1.9 3.2 %
    20 423 164 K 5.0 34.0 %
    21 446 187 L <0.1 0.1 %
    22 449 190 R 33.8 30.1 %
    23 450 191 L 0.2 1.3 %
    24 451 192 R 40.7 41.5 %
    25 452 193 L 6.2 54.5 %
    26 453 194 G 34.2 64.7 %
    27 454 195 L 14.8 75.2 %
    28 455 196 A 39.5 60.6 %
    29 456 197 E 4.9 12.2 %
    30 457 198 Q 51.2 55.0 %
    31 458 199 S 12.6 100.0 %
    32 504 245 K 10.9 19.1 %
    33 546 287 H 36.9 66.9 %
    34 547 288 P 9.3 12.6 %
    35 557 298 R 25.9 25.2 %
    36 568 309 K 2.4 37.8 %
    37 570 311 D 2.7 11.6 %
    38 571 312 G 11.3 91.4 %
    39 572 313 Q 39.9 80.0 %
    40 573 314 R 14.2 88.4 %
    41 588 329 S 22.0 93.2 %
    42 589 330 R 45.8 52.0 %
    43 590 331 N 28.1 29.0 %
    44 592 333 E 29.2 58.8 %
    45 594 335 N 5.3 23.0 %
    46 621 362 E 1.9 43.0 %
    47 635 376 F 37.7 67.5 %
    48 636 377 Q 33.7 42.4 %
    49 639 380 T 41.3 63.1 %
    50 640 381 T 35.2 38.9 %
    51 641 382 R 8.3 45.9 %
    52 642 383 K 47.3 30.7 %
    53 643 384 R 96.9 55.5 %
    54 644 385 K 55.6 35.6 %
    55 720 461 E 5.6 32.5 %
    56 737 478 K 4.0 2.9 %
    57 738 479 R 48.1 33.7 %
    58 739 480 S 14.8 35.4 %
    59 740 481 H 5.2 8.3 %
    60 744 485 K 17.8 67.2 %
    61 746 487 K 10.4 74.3 %
    62 748 489 D 2.3 38.9 %
    63 749 490 Y 32.6 58.7 %
    64 765 506 Y 4.4 16.2 %
    65 766 507 L 2.9 5.1 %
    66 767 508 G 3.4 87.5 %
    67 768 509 R 30.6 33.8 %
    68 769 510 G 10.4 58.1 %
    69 770 511 K 84.6 48.7 %
    70 771 512 R 36.6 59.8 %
    71 776 517 G 19.0 98.0 %
    72 777 518 G 10.9 86.5 %
    73 778 519 F <0.1 90.0 %
    74 794 535 C 8.8 100.0 %
    75 795 536 K 63.2 70.5 %
    76 796 537 L 8.4 100.0 %
    77 797 538 G 35.6 99.8 %
    78 798 539 T 58.2 92.6 %
    79 799 540 G 34.9 87.0 %
    80 800 541 F 12.6 92.6 %
    81 801 542 S 27.4 50.5 %
    82 802 543 D 40.8 39.6 %
    83 803 544 E 1.6 1.2 %
    84 804 545 E 0.4 0.6 %
    85 845 586 K 0.9 5.0 %
    86 850 591 S 22.1 71.6 %
    87 851 592 L 7.8 19.4 %
    88 852 593 S 13.6 100.0 %
    89 853 594 P 41.7 39.8 %
    90 854 595 I 7.8 11.1 %
    91 855 596 Y 23.8 97.2 %
    92 866 607 K 8.0 9.4 %
    93 869 610 S 18.7 100.0 %
    94 870 611 L 12.4 100.0 %
    95 871 612 R 22.3 45.5 %
    96 872 613 F 89.2 95.8 %
    97 873 614 P 29.6 95.1 %
    98 874 615 R 48.4 99.5 %
    99 875 616 F <0.1 1.6 %
    100 876 617 I 4.5 6.1 %

  • Interface residues in 6p0a_D_B_C

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 9:D1 G 51.2 22.2 %
    2 2 10:D1 T 68.6 39.6 %
    3 3 11:D1 C 100.5 59.6 %
    4 4 12:D1 C 92.9 62.3 %
    5 5 13:D1 G 92.6 49.2 %
    6 6 14:D1 A 143.5 86.8 %
    7 7 15:D1 C 103.0 61.5 %
    8 8 16:D1 G 118.5 65.5 %
    9 9 17:D1 A 97.4 71.1 %
    10 10 18:D1 C 87.8 57.9 %
    11 11 19:D1 G 100.1 60.8 %
    12 12 20:D1 C 92.9 58.6 %
    13 13 21:D1 A 79.1 51.6 %
    14 14 22:D1 T 24.8 12.2 %
    15 15 23:D1 C 71.8 43.5 %
    16 16 24:D1 A 61.4 40.7 %
    17 25 9:B1 G 74.0 40.7 %
    18 26 10:B1 C 72.9 43.9 %
    19 27 11:B1 G 54.5 37.9 %
    20 28 12:B1 T 110.1 68.0 %
    21 29 13:B1 C 121.4 83.9 %
    22 30 1:C1 G 62.5 56.3 %
    23 31 2:C1 T 111.1 74.6 %
    24 32 3:C1 C 85.1 50.7 %
    25 33 4:C1 G 62.2 32.2 %
    26 34 5:C1 G 52.2 30.9 %
    27 35 6:C1 A 25.1 14.3 %
    28 36 7:C1 C 49.8 17.6 %

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 25.1
2 303 44 S 36 7:C1 C 17.5 H-bond
3 304 45 A 36 7:C1 C 25.6
4 305 46 R 3 11:D1 C 36.1
5 305 46 R 4 12:D1 C 8.5
6 305 46 R 36 7:C1 C 5.8
7 306 47 L 36 7:C1 C 0.9
8 346 87 E 26 10:B1 C 33.8
9 346 87 E 27 11:B1 G 12.7
10 347 88 L 26 10:B1 C 11.6
11 348 89 G 25 9:B1 G 16.9
12 348 89 G 26 10:B1 C 10.1 H-bond
13 349 90 V 25 9:B1 G 6.2
14 349 90 V 26 10:B1 C 13.9
15 350 91 G 25 9:B1 G 26.2
16 350 91 G 26 10:B1 C 0.4
17 351 92 D 25 9:B1 G 5.3
18 352 93 G 25 9:B1 G 7.5
19 353 94 V 25 9:B1 G 3.1
20 415 156 T 14 22:D1 T 0.4
21 415 156 T 15 23:D1 C 13.9
22 416 157 G 15 23:D1 C 23.6 H-bond
23 416 157 G 16 24:D1 A 2.1
24 417 158 S 15 23:D1 C 4.7
25 417 158 S 16 24:D1 A 11.4
26 418 159 A 16 24:D1 A 16.5 H-bond
27 419 160 S 15 23:D1 C 12.3
28 419 160 S 16 24:D1 A 3.4
29 420 161 T 15 23:D1 C 12.3
30 420 161 T 16 24:D1 A 26.2 H-bond
31 421 162 A 16 24:D1 A 1.9
32 423 164 K 15 23:D1 C 5.0
33 446 187 L 26 10:B1 C <0.1
34 449 190 R 6 14:D1 A 18.4
35 449 190 R 7 15:D1 C 15.4 H-bond
36 450 191 L 5 13:D1 G 0.2
37 451 192 R 5 13:D1 G 16.0
38 451 192 R 6 14:D1 A 24.7
39 452 193 L 5 13:D1 G 6.2
40 453 194 G 4 12:D1 C 18.3
41 453 194 G 5 13:D1 G 15.9 H-bond
42 454 195 L 4 12:D1 C 5.6
43 454 195 L 5 13:D1 G 9.2
44 455 196 A 4 12:D1 C 26.6 H-bond
45 455 196 A 5 13:D1 G 12.8
46 456 197 E 4 12:D1 C 4.9
47 457 198 Q 3 11:D1 C 37.4
48 457 198 Q 4 12:D1 C 13.8 H-bond
49 458 199 S 3 11:D1 C 1.1
50 458 199 S 4 12:D1 C 11.5 H-bond
51 504 245 K 3 11:D1 C 10.9
52 546 287 H 1 9:D1 G 8.5
53 546 287 H 2 10:D1 T 28.4 H-bond
54 547 288 P 31 2:C1 T 2.0
55 547 288 P 32 3:C1 C 7.3
56 557 298 R 1 9:D1 G 25.7
57 557 298 R 2 10:D1 T 0.1
58 568 309 K 30 1:C1 G 2.4
59 570 311 D 29 13:B1 C 2.7
60 571 312 G 29 13:B1 C 11.3
61 572 313 Q 28 12:B1 T 31.0
62 572 313 Q 29 13:B1 C 8.9
63 573 314 R 28 12:B1 T <0.1
64 573 314 R 29 13:B1 C 14.2 H-bond
65 588 329 S 28 12:B1 T 20.5 H-bond
66 588 329 S 29 13:B1 C 1.4
67 589 330 R 28 12:B1 T 0.9
68 589 330 R 29 13:B1 C 23.7
69 589 330 R 30 1:C1 G 21.2
70 590 331 N 28 12:B1 T 24.2 H-bond
71 590 331 N 29 13:B1 C 3.9
72 592 333 E 27 11:B1 G 19.5
73 592 333 E 28 12:B1 T 9.7
74 594 335 N 28 12:B1 T 5.3
75 621 362 E 29 13:B1 C 1.9
76 635 376 F 9 17:D1 A 3.8
77 635 376 F 28 12:B1 T 14.5
78 635 376 F 29 13:B1 C 19.4
79 636 377 Q 10 18:D1 C 12.2
80 636 377 Q 11 19:D1 G 21.6 H-bond
81 639 380 T 11 19:D1 G 29.3
82 639 380 T 12 20:D1 C 7.0
83 639 380 T 27 11:B1 G 1.1
84 639 380 T 28 12:B1 T 3.9
85 640 381 T 11 19:D1 G 11.9
86 640 381 T 12 20:D1 C 23.3
87 641 382 R 12 20:D1 C 8.3
88 642 383 K 12 20:D1 C 25.2
89 642 383 K 13 21:D1 A 22.0 H-bond
90 643 384 R 11 19:D1 G 8.9
91 643 384 R 12 20:D1 C 29.0 H-bond
92 643 384 R 13 21:D1 A 25.8 H-bond
93 643 384 R 25 9:B1 G 8.8
94 643 384 R 26 10:B1 C 3.2
95 643 384 R 27 11:B1 G 21.2
96 644 385 K 13 21:D1 A 31.2
97 644 385 K 14 22:D1 T 24.4
98 720 461 E 29 13:B1 C 5.6
99 737 478 K 2 10:D1 T 4.0
100 738 479 R 1 9:D1 G 17.0
101 738 479 R 2 10:D1 T 31.0 H-bond
102 739 480 S 2 10:D1 T 0.2
103 739 480 S 3 11:D1 C 14.6
104 740 481 H 2 10:D1 T 4.8
105 740 481 H 3 11:D1 C 0.4
106 744 485 K 30 1:C1 G 1.9
107 744 485 K 31 2:C1 T 15.9 H-bond
108 746 487 K 30 1:C1 G 0.9
109 746 487 K 31 2:C1 T 9.5
110 748 489 D 31 2:C1 T 2.3
111 748 489 D 32 3:C1 C <0.1
112 749 490 Y 31 2:C1 T 21.9 H-bond
113 749 490 Y 32 3:C1 C 10.7
114 765 506 Y 8 16:D1 G 4.4
115 766 507 L 7 15:D1 C 2.9
116 767 508 G 7 15:D1 C 3.4
117 768 509 R 6 14:D1 A 9.6 H-bond
118 768 509 R 7 15:D1 C 21.0 H-bond
119 769 510 G 6 14:D1 A 10.4
120 770 511 K 4 12:D1 C 3.6
121 770 511 K 5 13:D1 G 32.0
122 770 511 K 6 14:D1 A 37.2 H-bond
123 770 511 K 33 4:C1 G 9.6
124 770 511 K 34 5:C1 G 2.2
125 771 512 R 5 13:D1 G 0.4
126 771 512 R 6 14:D1 A 30.9
127 771 512 R 7 15:D1 C 3.7
128 771 512 R 33 4:C1 G 1.7
129 776 517 G 7 15:D1 C 19.0
130 777 518 G 7 15:D1 C 6.5
131 777 518 G 8 16:D1 G 4.4
132 778 519 F 8 16:D1 G <0.1
133 794 535 C 8 16:D1 G 0.5
134 794 535 C 9 17:D1 A 8.4
135 795 536 K 8 16:D1 G 43.3 H-bond
136 795 536 K 9 17:D1 A 19.9 H-bond
137 796 537 L 7 15:D1 C 0.1
138 796 537 L 8 16:D1 G 8.3
139 797 538 G 6 14:D1 A 4.0
140 797 538 G 7 15:D1 C 23.3
141 797 538 G 8 16:D1 G 8.2
142 798 539 T 6 14:D1 A 8.2
143 798 539 T 7 15:D1 C 7.7
144 798 539 T 8 16:D1 G 2.8
145 798 539 T 30 1:C1 G 4.6
146 798 539 T 31 2:C1 T 17.6
147 798 539 T 32 3:C1 C 17.2
148 799 540 G 32 3:C1 C 16.8
149 799 540 G 33 4:C1 G 18.0
150 800 541 F 33 4:C1 G 12.6
151 801 542 S 33 4:C1 G 16.0
152 801 542 S 34 5:C1 G 11.3
153 802 543 D 33 4:C1 G 3.8
154 802 543 D 34 5:C1 G 37.0 H-bond
155 803 544 E 34 5:C1 G 1.6
156 804 545 E 33 4:C1 G 0.4
157 845 586 K 32 3:C1 C 0.9
158 850 591 S 9 17:D1 A 6.7
159 850 591 S 10 18:D1 C 15.4 H-bond
160 851 592 L 10 18:D1 C 5.5
161 851 592 L 11 19:D1 G 2.2
162 852 593 S 10 18:D1 C 13.6 H-bond
163 853 594 P 10 18:D1 C 23.5
164 853 594 P 11 19:D1 G 18.3
165 854 595 I 9 17:D1 A 1.7
166 854 595 I 10 18:D1 C 6.0
167 855 596 Y 9 17:D1 A 18.8 H-bond
168 855 596 Y 10 18:D1 C 5.0
169 866 607 K 11 19:D1 G 8.0
170 869 610 S 9 17:D1 A 12.2
171 869 610 S 10 18:D1 C 6.5
172 870 611 L 9 17:D1 A 12.4
173 871 612 R 8 16:D1 G 2.6
174 871 612 R 9 17:D1 A 6.6
175 871 612 R 29 13:B1 C 13.2
176 872 613 F 8 16:D1 G 20.5
177 872 613 F 9 17:D1 A 1.7
178 872 613 F 29 13:B1 C 15.2
179 872 613 F 30 1:C1 G 31.6
180 872 613 F 31 2:C1 T 20.2
181 873 614 P 8 16:D1 G 23.5
182 873 614 P 9 17:D1 A 5.2
183 873 614 P 31 2:C1 T 0.9
184 874 615 R 31 2:C1 T 20.8
185 874 615 R 32 3:C1 C 27.6 H-bond
186 875 616 F 32 3:C1 C <0.1
187 876 617 I 32 3:C1 C 4.5

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A6p0a_A1001MG 48.718.6
B6p0a_D_B_C101AMP 48.8305.1

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

    Result domain: 6p0a_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: 68% (68/100).

    Identities = 43% (29/68), Positive = 57% (39/68), Gaps = 4% (3/68).

    Query: 480 PVQPMLAEACKSVEYAMKKCPNGMFS-EIKYDGERVQVHK-NGDHFSYFSRSLKPVLPHK 537

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

    6p0a_A: 280 PLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQE----DN 335

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


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

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

    6p0a_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+ + +

    6p0a_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 +

    6p0a_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 +++++

    6p0a_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 +

    6p0a_A: 570 AVIPDHWL-DP--SAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPE 626

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


    Query: 818 SATNLPQLKELYQ 830

    AT Q+ LY+

    6p0a_A: 627 QATTSAQVACLYR 639

    dssp: H--EHHHHHHHHH


    Download alignment FASTA file