Interaction between DNA ligase I (LIG1) (d1x9na3) and DNA ligase I (LIG1) (d1x9na2)
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: 300.31 Å2
Number of inter-residue contacts at the interface: 25
Number of H-bonds: 3
Number of salt bridges: 3
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 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 %
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Interface residues in d1x9na2
No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, % 1 754 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 %
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 | 570 | 37 | D | 848 | 95 | D | 3.0 | |
2 | 570 | 37 | D | 871 | 118 | R | 20.1 | H-bond, Salt bridge |
3 | 635 | 102 | F | 871 | 118 | R | 26.3 | |
4 | 636 | 103 | Q | 849 | 96 | L | 0.3 | |
5 | 636 | 103 | Q | 850 | 97 | S | 23.4 | |
6 | 636 | 103 | Q | 851 | 98 | L | 18.6 | |
7 | 636 | 103 | Q | 897 | 144 | Y | 1.8 | |
8 | 720 | 187 | E | 847 | 94 | A | 4.2 | |
9 | 720 | 187 | E | 848 | 95 | D | 3.8 | |
10 | 720 | 187 | E | 871 | 118 | R | 8.8 | |
11 | 720 | 187 | E | 872 | 119 | F | 10.0 | |
12 | 746 | 213 | K | 874 | 121 | R | 5.7 | |
13 | 747 | 214 | K | 847 | 94 | A | 16.3 | |
14 | 747 | 214 | K | 848 | 95 | D | 18.9 | H-bond, Salt bridge |
15 | 747 | 214 | K | 900 | 147 | Q | 0.6 | |
16 | 748 | 215 | D | 754 | 1 | G | 15.7 | |
17 | 748 | 215 | D | 845 | 92 | K | 13.4 | |
18 | 748 | 215 | D | 846 | 93 | C | 3.6 | |
19 | 748 | 215 | D | 847 | 94 | A | 13.4 | |
20 | 748 | 215 | D | 874 | 121 | R | 17.7 | H-bond, Salt bridge |
21 | 749 | 216 | Y | 845 | 92 | K | 12.2 | |
22 | 751 | 218 | D | 754 | 1 | G | 10.5 | |
23 | 753 | 220 | V | 754 | 1 | G | 25.7 | |
24 | 753 | 220 | V | 756 | 3 | T | 10.9 | |
25 | 753 | 220 | V | 845 | 92 | K | 15.3 |
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: 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: 90% (9/10).
Identities = 78% (7/9), Positive = 89% (8/9), Gaps = 0% (0/9).
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