Interaction between DNA ligase I (LIG1) (d1x9na2) 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: d1x9na2

    Title: DNA ligase I (LIG1)

    Source organism: Homo sapiens

    Number of residues: 148

    SCOP family: b.40.4.6

  • 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: 849.97 Å2

Number of inter-residue contacts at the interface: 65

Number of H-bonds: 9

  • Pairwise interaction

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  • Biological assembly

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

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Create a structural model for this interaction

  • Interface residues in d1x9na2

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 765 12 Y 3.3 12.2 %
    2 766 13 L 3.1 2.9 %
    3 767 14 G 4.2 28.7 %
    4 768 15 R 40.0 19.3 %
    5 769 16 G 17.0 26.0 %
    6 770 17 K 80.3 49.3 %
    7 771 18 R 41.8 63.3 %
    8 776 23 G 16.7 93.3 %
    9 777 24 G 7.1 82.7 %
    10 778 25 F 0.2 22.0 %
    11 794 41 C 8.2 100.0 %
    12 795 42 K 64.2 68.7 %
    13 796 43 L 5.9 99.2 %
    14 797 44 G 32.5 96.6 %
    15 798 45 T 54.6 89.6 %
    16 799 46 G 30.9 78.5 %
    17 800 47 F 13.2 87.1 %
    18 801 48 S 26.0 51.1 %
    19 802 49 D 41.4 34.9 %
    20 803 50 E 1.9 1.3 %
    21 850 97 S 24.9 41.1 %
    22 851 98 L 12.1 32.4 %
    23 852 99 S 16.5 98.4 %
    24 853 100 P 34.4 31.5 %
    25 854 101 I 3.3 4.9 %
    26 855 102 Y 26.1 68.5 %
    27 866 113 K 4.1 4.6 %
    28 869 116 S 20.3 100.0 %
    29 870 117 L 12.3 100.0 %
    30 871 118 R 31.8 26.5 %
    31 872 119 F 90.4 83.7 %
    32 873 120 P 29.2 87.7 %
    33 874 121 R 52.3 55.3 %

  • Interface residues in 1x9n_D_B_C

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 12 12:D1 C 4.2 2.3 %
    2 13 13:D1 G 32.1 16.3 %
    3 14 14:D1 A 111.5 62.8 %
    4 15 15:D1 C 92.7 52.3 %
    5 16 16:D1 G 112.8 61.7 %
    6 17 17:D1 A 90.3 64.9 %
    7 18 18:D1 C 78.0 51.5 %
    8 19 19:D1 G 27.9 15.3 %
    9 39 13:B1 DOC 35.0 22.3 %
    10 40 1:C1 G 32.4 28.6 %
    11 41 2:C1 T 60.5 41.5 %
    12 42 3:C1 C 65.4 37.6 %
    13 43 4:C1 G 55.3 30.4 %
    14 44 5:C1 G 51.8 30.1 %

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
1 765 12 Y 16 16:D1 G 3.3
2 766 13 L 15 15:D1 C 3.1
3 767 14 G 15 15:D1 C 4.2
4 768 15 R 14 14:D1 A 12.5 H-bond
5 768 15 R 15 15:D1 C 27.4
6 769 16 G 14 14:D1 A 17.0
7 770 17 K 12 12:D1 C 4.2
8 770 17 K 13 13:D1 G 30.3 H-bond
9 770 17 K 14 14:D1 A 37.5 H-bond
10 770 17 K 43 4:C1 G 8.3
11 771 18 R 13 13:D1 G 1.8
12 771 18 R 14 14:D1 A 33.5
13 771 18 R 15 15:D1 C 6.5
14 776 23 G 15 15:D1 C 16.7
15 777 24 G 15 15:D1 C 3.8
16 777 24 G 16 16:D1 G 3.3
17 778 25 F 16 16:D1 G 0.2
18 794 41 C 16 16:D1 G <0.1
19 794 41 C 17 17:D1 A 8.2
20 795 42 K 16 16:D1 G 43.1
21 795 42 K 17 17:D1 A 21.1 H-bond
22 796 43 L 16 16:D1 G 5.9
23 797 44 G 14 14:D1 A 1.2
24 797 44 G 15 15:D1 C 22.2
25 797 44 G 16 16:D1 G 9.0
26 798 45 T 14 14:D1 A 9.7
27 798 45 T 15 15:D1 C 8.8
28 798 45 T 40 1:C1 G 1.8
29 798 45 T 41 2:C1 T 12.8
30 798 45 T 42 3:C1 C 21.6
31 799 46 G 42 3:C1 C 14.5
32 799 46 G 43 4:C1 G 16.4
33 800 47 F 43 4:C1 G 13.2
34 801 48 S 43 4:C1 G 13.6
35 801 48 S 44 5:C1 G 12.4
36 802 49 D 43 4:C1 G 3.9
37 802 49 D 44 5:C1 G 37.5 H-bond
38 803 50 E 44 5:C1 G 1.9
39 850 97 S 17 17:D1 A 5.0
40 850 97 S 18 18:D1 C 19.9 H-bond
41 851 98 L 18 18:D1 C 5.4
42 851 98 L 19 19:D1 G 6.7
43 852 99 S 18 18:D1 C 16.5 H-bond
44 853 100 P 18 18:D1 C 17.4
45 853 100 P 19 19:D1 G 17.1
46 854 101 I 18 18:D1 C 3.3
47 855 102 Y 17 17:D1 A 20.7 H-bond
48 855 102 Y 18 18:D1 C 5.4
49 866 113 K 19 19:D1 G 4.1
50 869 116 S 17 17:D1 A 10.1
51 869 116 S 18 18:D1 C 10.1
52 870 117 L 17 17:D1 A 12.3
53 871 118 R 16 16:D1 G 4.0
54 871 118 R 17 17:D1 A 6.6
55 871 118 R 39 13:B1 DOC 21.2
56 872 119 F 16 16:D1 G 21.8
57 872 119 F 17 17:D1 A 0.7
58 872 119 F 39 13:B1 DOC 13.8
59 872 119 F 40 1:C1 G 30.6
60 872 119 F 41 2:C1 T 23.6
61 873 120 P 16 16:D1 G 22.3
62 873 120 P 17 17:D1 A 5.6
63 873 120 P 41 2:C1 T 1.3
64 874 121 R 41 2:C1 T 22.9
65 874 121 R 42 3:C1 C 29.4 H-bond

Analyse interface in VoroContacts server

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

    Result domain: d1x9na2; DNA ligase I (LIG1)

    Alignment data:

    Expectation value = 2.20e-15, Score = 77 bits (188),

    Identities = 34% (52/152), Positive = 51% (78/152), Gaps = 10% (15/152).

    Interface alignment data:

    Interface residues in alignment: 100% (33/33).

    Identities = 39% (13/33), Positive = 55% (18/33), Gaps = 0% (0/33).

    Query: 687 ADTADLVVLGAFYGQGSKGGMMSIFLMGCYDPGSQKWCTVTKCAGGHDDATLARLQNELD 746

    DT DLVV+GA+ G+G + G FL+ YD S++ + K G D L L

    d1x9na2: 1 GDTLDLVVIGAYLGRGKRAGRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLK 60

    dssp: -EEEEEEEEEEEEE----E--EEEEEEEEEE----EEEEEEEE-----HHHHHHHHHHHH


    Query: 747 MVKISKDPSKIPSWLKVNKIYYPDFIVPDPKKAAVWEITGAEFSKSEAHTA--------D 798

    + + PS P +++++ PD + DP +AVWE+ A+ S S + A

    d1x9na2: 61 ALVL---PSPRP-YVRIDGAVIPDHWL-DP--SAVWEVKCADLSLSPIYPAARGLVDSDK 113

    dssp: H-EE ----- -EE--------EEE -- --EEEEEE-EEEEE--------------


    Query: 799 GISIRFPRCTRIRDDKDWKSATNLPQLKELYQ 830

    GIS+RFPR R+R+DK + AT Q+ LY+

    d1x9na2: 114 GISLRFPRFIRVREDKQPEQATTSAQVACLYR 145

    dssp: EEEEE--EEEEE-----HHH--EHHHHHHHHH


    Download alignment FASTA file