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
Structural properties
Hetero-dimer interface properties
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
Experimental structure
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Pairwise interaction
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Biological assembly
Homomer, 1 protein, 3 domains, 1 nucleic acid.
Interface structure modeling
Residues at the interaction interface
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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 %
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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 %
Inter-residue contacts at the interaction interface
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 |
Sequence alignments
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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