Interaction between DNA ligase I (LIG1) (d1x9na2) and DNA ligase I (LIG1) (d1x9na1)

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: d1x9na1

    Title: DNA ligase I (LIG1)

    Source organism: Homo sapiens

    Number of residues: 272 (8 missing in structure)

    SCOP family: a.235.1.1

Buried interface area: 252.59 Å2

Number of inter-residue contacts at the interface: 23

Number of H-bonds: 1

Number of salt bridges: 1

  • Pairwise interaction

  • Biological assembly

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


  • Interface residues in d1x9na2

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 766 13 L 41.8 42.5 %
    2 767 14 G 10.4 82.8 %
    3 768 15 R 97.6 50.2 %
    4 769 16 G 47.8 82.4 %
    5 770 17 K 19.5 10.3 %
    6 772 19 A 16.5 40.2 %
    7 773 20 G 17.7 22.4 %
    8 833 80 D 1.2 1.5 %

  • Interface residues in d1x9na1

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 351 90 D 24.6 27.8 %
    2 374 113 A 31.9 39.5 %
    3 375 114 E 29.2 23.3 %
    4 376 115 K 12.9 11.8 %
    5 377 116 G 41.8 78.8 %
    6 378 117 D 1.0 3.7 %
    7 379 118 V 3.7 21.7 %
    8 449 188 R 54.5 36.6 %
    9 451 190 R 53.1 30.2 %

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. in chain B sequence Residue in chain B Contact area, Å2 Contact type
1 766 13 L 374 113 A 27.3
2 766 13 L 375 114 E 14.5
3 767 14 G 374 113 A 3.1
4 767 14 G 375 114 E 1.0
5 767 14 G 377 116 G 6.3
6 768 15 R 351 90 D 24.6 H-bond, Salt bridge
7 768 15 R 374 113 A 0.3
8 768 15 R 377 116 G 19.1
9 768 15 R 379 118 V 3.7
10 768 15 R 449 188 R 49.9
11 769 16 G 377 116 G 9.2
12 769 16 G 378 117 D 0.5
13 769 16 G 449 188 R 4.6
14 769 16 G 451 190 R 33.5
15 770 17 K 451 190 R 19.5
16 772 19 A 376 115 K 9.7
17 772 19 A 377 116 G 6.4
18 772 19 A 378 117 D 0.4
19 772 19 A 451 190 R <0.1
20 773 20 G 375 114 E 13.7
21 773 20 G 376 115 K 3.1
22 773 20 G 377 116 G 0.9
23 833 80 D 374 113 A 1.2

  • 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% (8/8).

    Identities = 50% (4/8), Positive = 62% (5/8), Gaps = 0% (0/8).

    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