Interaction between DNA ligase I (LIG1) (d1x9na3) 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: d1x9na3

    Title: DNA ligase I (LIG1)

    Source organism: Homo sapiens

    Number of residues: 220

    SCOP family: d.142.2.1

  • 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: 612.45 Å2

Number of inter-residue contacts at the interface: 50

Number of H-bonds: 3

Number of salt bridges: 2

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

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

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Create a structural model for this interaction

  • Interface residues in d1x9na3

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 534 1 L 71.8 81.1 %
    2 535 2 S 8.3 14.9 %
    3 538 5 I 75.9 75.2 %
    4 539 6 P 34.3 94.9 %
    5 540 7 L 23.0 82.7 %
    6 541 8 K 75.9 63.4 %
    7 587 54 F 9.7 76.9 %
    8 590 57 N 10.5 11.2 %
    9 591 58 Q 47.8 86.1 %
    10 592 59 E 37.0 34.9 %
    11 593 60 D 21.2 26.6 %
    12 669 136 S 2.2 4.3 %
    13 671 138 V 22.7 85.2 %
    14 672 139 R 28.8 16.4 %
    15 733 200 Y 3.3 61.3 %
    16 734 201 E 16.1 51.7 %
    17 735 202 I 25.6 59.9 %
    18 736 203 A 68.3 72.3 %
    19 737 204 K 30.2 19.3 %

  • Interface residues in d1x9na1

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 341 80 P 51.0 56.3 %
    2 342 81 Q 67.1 61.2 %
    3 344 83 G 12.9 24.4 %
    4 346 85 E 4.3 3.4 %
    5 456 195 E 21.1 29.4 %
    6 501 240 MSE 48.7 38.9 %
    7 504 243 K 11.7 20.8 %
    8 505 244 Q 74.4 84.0 %
    9 507 246 F 11.0 50.4 %
    10 508 247 C 65.0 82.3 %
    11 509 248 E 83.2 74.1 %
    12 510 249 V 18.0 91.4 %
    13 511 250 P 51.2 95.3 %
    14 512 251 D 9.6 48.4 %
    15 515 254 R 35.5 23.5 %
    16 533 272 K 47.9 26.3 %

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
1 534 1 L 509 248 E 34.1
2 534 1 L 510 249 V 2.0
3 534 1 L 533 272 K 35.7
4 535 2 S 509 248 E 0.1
5 535 2 S 510 249 V 0.3
6 535 2 S 533 272 K 7.9
7 538 5 I 342 81 Q 3.2
8 538 5 I 509 248 E 4.2
9 538 5 I 510 249 V 15.7
10 538 5 I 511 250 P 3.5
11 538 5 I 512 251 D 9.6
12 538 5 I 515 254 R 35.5
13 538 5 I 533 272 K 4.3
14 539 6 P 341 80 P <0.1
15 539 6 P 342 81 Q 19.6
16 539 6 P 509 248 E 2.6
17 539 6 P 511 250 P 12.2
18 540 7 L 508 247 C 4.6
19 540 7 L 509 248 E 12.9
20 540 7 L 511 250 P 5.5
21 541 8 K 456 195 E 21.1 H-bond, Salt bridge
22 541 8 K 507 246 F 11.0
23 541 8 K 508 247 C 27.4 H-bond
24 541 8 K 511 250 P 16.4
25 587 54 F 342 81 Q 9.7
26 590 57 N 341 80 P 10.5
27 591 58 Q 341 80 P 23.2
28 591 58 Q 342 81 Q 10.9
29 591 58 Q 511 250 P 13.6
30 592 59 E 341 80 P 17.2
31 592 59 E 342 81 Q 2.6
32 592 59 E 344 83 G 12.9
33 592 59 E 346 85 E 4.3
34 593 60 D 341 80 P <0.1
35 593 60 D 342 81 Q 21.1
36 669 136 S 509 248 E 2.2
37 671 138 V 505 244 Q 5.5
38 671 138 V 509 248 E 17.2
39 672 139 R 505 244 Q 18.8
40 672 139 R 509 248 E 9.9 Salt bridge
41 733 200 Y 505 244 Q 3.3
42 734 201 E 505 244 Q 16.1
43 735 202 I 505 244 Q 4.5
44 735 202 I 508 247 C 21.1
45 736 203 A 501 240 MSE 22.3
46 736 203 A 504 243 K 11.7
47 736 203 A 505 244 Q 22.4 H-bond
48 736 203 A 508 247 C 11.9
49 737 204 K 501 240 MSE 26.4
50 737 204 K 505 244 Q 3.8

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: 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: 84% (16/19).

    Identities = 38% (6/16), Positive = 69% (11/16), Gaps = 0% (0/16).

    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