Interaction between DNA ligase I (LIG1) (d1x9na3) and template DNA/dideoxy terminated DNA/5'-phosphorylated DNA (1x9n_D_B_C)

PDB and SCOP data

PDB ID: 1x9n (all binary interactions in this PDB entry)

Title: Crystal Structure of Human DNA Ligase I bound to 5'-adenylated, nicked DNA

Release date: 2004-11-30

Resolution: 3.0 Å

  • Chain A: d1x9na3

    Title: DNA ligase I (LIG1)

    Source organism: Homo sapiens

    Number of residues: 220

    SCOP family: d.142.2.1

  • Chain B: 1x9n_D_B_C

    Title: template DNA/dideoxy terminated DNA/5'-phosphorylated DNA

    Number of residues: 56

    Note: Residues of nucleic acid domain are renumbered to avoid repeating the same residue numbers from different PDB chains.

Buried interface area: 616.95 Å2

Number of inter-residue contacts at the interface: 51

Number of H-bonds: 11

  • Pairwise interaction

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  • Biological assembly

    Homomer, 1 protein, 3 domains, 1 nucleic acid.

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  • Interface residues in d1x9na3

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 546 13 H 9.5 15.1 %
    2 547 14 P 2.7 4.7 %
    3 557 24 R 33.5 28.4 %
    4 568 35 K 5.8 63.9 %
    5 570 37 D 6.3 12.6 %
    6 571 38 G 10.7 89.8 %
    7 572 39 Q 36.2 91.9 %
    8 573 40 R 13.1 74.9 %
    9 588 55 S 16.9 80.7 %
    10 589 56 R 40.4 39.4 %
    11 590 57 N 27.3 28.8 %
    12 592 59 E 44.0 40.0 %
    13 594 61 N 14.9 53.5 %
    14 597 64 K 4.1 10.8 %
    15 621 88 E 2.4 62.4 %
    16 635 102 F 45.5 52.1 %
    17 636 103 Q 39.5 28.3 %
    18 639 106 T 39.8 54.0 %
    19 640 107 T 31.6 35.4 %
    20 641 108 R 11.0 41.5 %
    21 642 109 K 42.4 26.2 %
    22 643 110 R 28.7 39.7 %
    23 644 111 K 24.8 28.1 %
    24 645 112 E <0.1 0.1 %
    25 720 187 E 14.1 20.4 %
    26 737 204 K 3.7 2.4 %
    27 738 205 R 20.1 16.9 %
    28 739 206 S 2.1 6.6 %
    29 740 207 H 7.1 7.9 %
    30 744 211 K 12.2 66.1 %
    31 746 213 K 26.2 37.9 %

  • Interface residues in 1x9n_D_B_C

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 8 8:D1 A 8.5 4.9 %
    2 9 9:D1 G 34.6 21.8 %
    3 10 10:D1 T 30.9 19.8 %
    4 11 11:D1 C 2.1 1.1 %
    5 17 17:D1 A 3.0 1.9 %
    6 18 18:D1 C 21.1 11.4 %
    7 19 19:D1 G 59.3 32.8 %
    8 20 20:D1 C 63.8 41.1 %
    9 21 21:D1 A 69.3 51.9 %
    10 22 22:D1 T 2.5 1.3 %
    11 37 11:B1 G 39.3 22.0 %
    12 38 12:B1 T 106.3 63.0 %
    13 39 13:B1 DOC 104.3 73.3 %
    14 40 1:C1 G 30.8 29.2 %
    15 41 2:C1 T 31.5 21.8 %
    16 42 3:C1 C 9.6 5.4 %

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
1 546 13 H 9 9:D1 G 9.5
2 547 14 P 42 3:C1 C 2.7
3 557 24 R 8 8:D1 A 8.5
4 557 24 R 9 9:D1 G 25.1
5 568 35 K 40 1:C1 G 5.8
6 570 37 D 39 13:B1 DOC 6.3
7 571 38 G 39 13:B1 DOC 10.7
8 572 39 Q 38 12:B1 T 24.9
9 572 39 Q 39 13:B1 DOC 11.4
10 573 40 R 39 13:B1 DOC 13.1 H-bond
11 588 55 S 38 12:B1 T 16.9 H-bond
12 589 56 R 38 12:B1 T 0.7
13 589 56 R 39 13:B1 DOC 24.0
14 589 56 R 40 1:C1 G 15.6
15 590 57 N 37 11:B1 G 6.1
16 590 57 N 38 12:B1 T 17.2 H-bond
17 590 57 N 39 13:B1 DOC 4.0
18 592 59 E 37 11:B1 G 31.3
19 592 59 E 38 12:B1 T 12.7
20 594 61 N 38 12:B1 T 14.9 H-bond
21 597 64 K 38 12:B1 T 4.1
22 621 88 E 39 13:B1 DOC 2.3
23 621 88 E 40 1:C1 G <0.1
24 635 102 F 17 17:D1 A 3.0
25 635 102 F 38 12:B1 T 14.8
26 635 102 F 39 13:B1 DOC 27.7
27 636 103 Q 18 18:D1 C 21.1 H-bond
28 636 103 Q 19 19:D1 G 18.5 H-bond
29 639 106 T 19 19:D1 G 31.7 H-bond
30 639 106 T 20 20:D1 C 6.3
31 639 106 T 37 11:B1 G 1.9
32 640 107 T 19 19:D1 G 9.1
33 640 107 T 20 20:D1 C 22.4
34 641 108 R 20 20:D1 C 11.0
35 642 109 K 20 20:D1 C 11.1
36 642 109 K 21 21:D1 A 31.3 H-bond
37 643 110 R 20 20:D1 C 13.1 H-bond
38 643 110 R 21 21:D1 A 15.6
39 644 111 K 21 21:D1 A 22.4 H-bond
40 644 111 K 22 22:D1 T 2.5
41 645 112 E 21 21:D1 A <0.1
42 720 187 E 39 13:B1 DOC 4.8
43 720 187 E 40 1:C1 G 9.3
44 737 204 K 10 10:D1 T 3.7
45 738 205 R 10 10:D1 T 20.1
46 739 206 S 10 10:D1 T <0.1
47 739 206 S 11 11:D1 C 2.1
48 740 207 H 10 10:D1 T 7.1
49 744 211 K 41 2:C1 T 12.2
50 746 213 K 41 2:C1 T 19.3 H-bond
51 746 213 K 42 3:C1 C 6.9

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
B1x9n_D_B_C100AMP 56.4312.9

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

    Result domain: d1x9na3; DNA ligase I (LIG1)

    Alignment data:

    Expectation value = 2.34e-27, Score = 114 bits (284),

    Identities = 33% (72/217), Positive = 50% (109/217), Gaps = 8% (18/217).

    Interface alignment data:

    Interface residues in alignment: 100% (31/31).

    Identities = 45% (14/31), Positive = 61% (19/31), Gaps = 13% (4/31).

    Query: 480 PVQPMLAEACKSVEYAMKKCPNGMFS-EIKYDGERVQVHK-NGDHFSYFSRSLKPVLPHK 537

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

    d1x9na3: 6 PLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQE----DN 61

    dssp: -----EEEEE--HHHHHHH-----EEEEEEE--EEEEEEE-----EEEE----- E-


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

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

    d1x9na3: 62 TGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQ 121

    dssp: ----HHHHH--HHHE------EEEEEEEEEE------E--HHHH---------HHH---E


    Query: 590 VCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIPNRIMFSEMKRVTKALDLADMITRV 649

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

    d1x9na3: 122 VCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQS 181

    dssp: EEEEEEEEEEE--EE-----HHHHHHHHHHHE--E---EEE--EE----HHHHHHHHHHH


    Query: 650 IQEGLEGLVLK--DVKGTYEPGKR--HWLKVKKDYLN 682

    +++ EGL++K DV TYE KR +WLK+KKDYL+

    d1x9na3: 182 VKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLD 218

    dssp: HH--EEEEEEEE-------------EEEEEEEHHHHH


    Download alignment FASTA file