Interaction between DNA ligase I (LIG1) (d1x9na2) and DNA ligase I (LIG1) (d1x9na3)

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: d1x9na3

    Title: DNA ligase I (LIG1)

    Source organism: Homo sapiens

    Number of residues: 220

    SCOP family: d.142.2.1

Buried interface area: 300.31 Å2

Number of inter-residue contacts at the interface: 25

Number of H-bonds: 3

Number of salt bridges: 3

  • Pairwise interaction

    Download PDB coordinates

    Download PyMOL visualization script

  • Biological assembly

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

    Download PDB coordinates


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, %
    1 754 1 G 51.9 75.4 %
    2 756 3 T 10.9 16.3 %
    3 845 92 K 41.0 73.1 %
    4 846 93 C 3.6 78.0 %
    5 847 94 A 33.9 75.4 %
    6 848 95 D 25.7 50.4 %
    7 849 96 L 0.3 3.9 %
    8 850 97 S 23.4 46.6 %
    9 851 98 L 18.6 49.4 %
    10 871 118 R 55.2 54.8 %
    11 872 119 F 10.0 7.9 %
    12 874 121 R 23.4 24.6 %
    13 897 144 Y 1.8 4.0 %
    14 900 147 Q 0.6 0.7 %

  • Interface residues in d1x9na3

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 570 37 D 23.1 47.2 %
    2 635 102 F 26.3 27.7 %
    3 636 103 Q 44.2 31.9 %
    4 720 187 E 26.7 37.5 %
    5 746 213 K 5.7 8.0 %
    6 747 214 K 35.8 37.1 %
    7 748 215 D 63.9 83.6 %
    8 749 216 Y 12.2 8.6 %
    9 751 218 D 10.5 8.7 %
    10 753 220 V 52.0 35.1 %

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. in chain B sequence Residue in chain B Contact area, Å2 Contact type
1 754 1 G 748 215 D 15.7
2 754 1 G 751 218 D 10.5
3 754 1 G 753 220 V 25.7
4 756 3 T 753 220 V 10.9
5 845 92 K 748 215 D 13.4
6 845 92 K 749 216 Y 12.2
7 845 92 K 753 220 V 15.3
8 846 93 C 748 215 D 3.6
9 847 94 A 720 187 E 4.2
10 847 94 A 747 214 K 16.3
11 847 94 A 748 215 D 13.4
12 848 95 D 570 37 D 3.0
13 848 95 D 720 187 E 3.8
14 848 95 D 747 214 K 18.9 H-bond, Salt bridge
15 849 96 L 636 103 Q 0.3
16 850 97 S 636 103 Q 23.4
17 851 98 L 636 103 Q 18.6
18 871 118 R 570 37 D 20.1 H-bond, Salt bridge
19 871 118 R 635 102 F 26.3
20 871 118 R 720 187 E 8.8
21 872 119 F 720 187 E 10.0
22 874 121 R 746 213 K 5.7
23 874 121 R 748 215 D 17.7 H-bond, Salt bridge
24 897 144 Y 636 103 Q 1.8
25 900 147 Q 747 214 K 0.6

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: 93% (13/14).

    Identities = 54% (7/13), Positive = 62% (8/13), Gaps = 0% (0/13).

    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