Interaction between DNA ligase 3 (3pc7_B) and DNA ligase 3 (3pc7_B)
PDB and SCOP data
PDB ID: 3pc7 (all binary interactions in this PDB entry)
Title: X-ray crystal structure of the DNA ligase III-alpha BRCT domain.
Release date: 2011-06-15
Resolution: 1.6 Å
Structural properties
Homo-dimer interface properties
Buried interface area: 547.68 Å2
Number of inter-residue contacts at the interface: 46
Number of H-bonds: 10
Number of salt bridges: 6
Experimental structure
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Pairwise interaction
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Biological assembly
Homomer, 2 proteins, 2 domains.
Interface structure modeling
Oligomer structure modeling
Residues at the interaction interface
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Interface residues in 3pc7_B
No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, % 1 846 12 V 0.7 0.3 % 2 847 13 L 93.1 79.8 % 3 848 14 L 6.3 9.7 % 4 849 15 D 14.3 12.8 % 5 860 26 P 8.7 9.2 % 6 865 31 F <0.1 0.2 % 7 866 32 S 0.6 0.8 % 8 869 35 R 69.5 82.1 % 9 870 36 R 111.8 76.8 % 10 871 37 Y 28.9 31.9 % 11 873 39 V 57.4 96.9 % 12 874 40 A 41.0 100.0 % 13 875 41 F 16.8 51.3 % 14 876 42 D 27.3 37.9 % 15 877 43 G 5.1 44.1 % 16 878 44 D 18.3 25.8 % 17 879 45 L 39.1 59.3 % 18 881 47 Q 2.5 6.0 % 19 883 49 F 6.2 3.3 %
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Interface residues in 3pc7_B
No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, % 1 846 12 V 0.7 0.3 % 2 847 13 L 93.1 79.8 % 3 848 14 L 6.3 9.7 % 4 849 15 D 14.3 12.8 % 5 860 26 P 8.7 9.2 % 6 865 31 F <0.1 0.2 % 7 866 32 S 0.6 0.8 % 8 869 35 R 69.5 82.1 % 9 870 36 R 111.8 76.8 % 10 871 37 Y 28.9 31.9 % 11 873 39 V 57.4 96.9 % 12 874 40 A 41.0 100.0 % 13 875 41 F 16.8 51.2 % 14 876 42 D 27.3 37.9 % 15 877 43 G 5.1 44.0 % 16 878 44 D 18.3 25.8 % 17 879 45 L 39.1 59.3 % 18 881 47 Q 2.5 6.0 % 19 883 49 F 6.2 3.3 %
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 | 846 | 12 | V | 871 | 37 | Y | 0.7 | |
2 | 847 | 13 | L | 847 | 13 | L | 11.6 | |
3 | 847 | 13 | L | 870 | 36 | R | 26.5 | |
4 | 847 | 13 | L | 871 | 37 | Y | 28.2 | |
5 | 847 | 13 | L | 874 | 40 | A | 11.4 | |
6 | 847 | 13 | L | 875 | 41 | F | 15.4 | |
7 | 848 | 14 | L | 870 | 36 | R | 6.3 | H-bond |
8 | 849 | 15 | D | 870 | 36 | R | 14.3 | H-bond, Salt bridge |
9 | 860 | 26 | P | 881 | 47 | Q | 2.5 | |
10 | 860 | 26 | P | 883 | 49 | F | 6.2 | |
11 | 865 | 31 | F | 878 | 44 | D | <0.1 | |
12 | 866 | 32 | S | 878 | 44 | D | 0.6 | |
13 | 869 | 35 | R | 873 | 39 | V | 17.4 | |
14 | 869 | 35 | R | 877 | 43 | G | 5.1 | |
15 | 869 | 35 | R | 878 | 44 | D | 17.7 | H-bond, Salt bridge |
16 | 869 | 35 | R | 879 | 45 | L | 29.3 | H-bond |
17 | 870 | 36 | R | 847 | 13 | L | 26.5 | |
18 | 870 | 36 | R | 848 | 14 | L | 6.3 | H-bond |
19 | 870 | 36 | R | 849 | 15 | D | 14.3 | H-bond, Salt bridge |
20 | 870 | 36 | R | 873 | 39 | V | 21.9 | |
21 | 870 | 36 | R | 874 | 40 | A | 14.1 | H-bond |
22 | 870 | 36 | R | 875 | 41 | F | 1.4 | |
23 | 870 | 36 | R | 876 | 42 | D | 27.3 | Salt bridge |
24 | 871 | 37 | Y | 846 | 12 | V | 0.7 | |
25 | 871 | 37 | Y | 847 | 13 | L | 28.2 | |
26 | 873 | 39 | V | 869 | 35 | R | 17.4 | |
27 | 873 | 39 | V | 870 | 36 | R | 21.9 | |
28 | 873 | 39 | V | 873 | 39 | V | 17.7 | |
29 | 873 | 39 | V | 874 | 40 | A | 0.3 | |
30 | 873 | 39 | V | 879 | 45 | L | 0.1 | |
31 | 874 | 40 | A | 847 | 13 | L | 11.4 | |
32 | 874 | 40 | A | 870 | 36 | R | 14.1 | H-bond |
33 | 874 | 40 | A | 873 | 39 | V | 0.3 | |
34 | 874 | 40 | A | 874 | 40 | A | 15.2 | |
35 | 875 | 41 | F | 847 | 13 | L | 15.4 | |
36 | 875 | 41 | F | 870 | 36 | R | 1.4 | |
37 | 876 | 42 | D | 870 | 36 | R | 27.3 | Salt bridge |
38 | 877 | 43 | G | 869 | 35 | R | 5.1 | |
39 | 878 | 44 | D | 865 | 31 | F | <0.1 | |
40 | 878 | 44 | D | 866 | 32 | S | 0.6 | |
41 | 878 | 44 | D | 869 | 35 | R | 17.7 | H-bond, Salt bridge |
42 | 879 | 45 | L | 869 | 35 | R | 29.3 | H-bond |
43 | 879 | 45 | L | 873 | 39 | V | 0.1 | |
44 | 879 | 45 | L | 879 | 45 | L | 9.7 | |
45 | 881 | 47 | Q | 860 | 26 | P | 2.5 | |
46 | 883 | 49 | F | 860 | 26 | P | 6.2 |
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: 3pc7_B; DNA ligase 3
Alignment data:
Expectation value = 4.10e-52, Score = 180 bits (455),
Identities = 98% (84/86), Positive = 99% (85/86), Gaps = 0% (0/86).
Interface alignment data:
Interface residues in alignment: 100% (19/19).
Identities = 100% (19/19), Positive = 100% (19/19), Gaps = 0% (0/19).
Query: 923 AADETLCQTKVLLDIFTGVRLYLPPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGSR 982
+ADETL QTKVLLDIFTGVRLYLPPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGSR
3pc7_B: 2 SADETLSQTKVLLDIFTGVRLYLPPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGSR 61
dssp: ---------EE--------HHHHHHHHHH---EE--HHHHHH--EE----
Query: 983 DKNPAAQQVSPEWIWACIRKRRLVAP 1008
DKNPAAQQVSPEWIWACIRKRRLVAP
3pc7_B: 62 DKNPAAQQVSPEWIWACIRKRRLVAP 87
dssp: ------EE--HHHHHHHHHH------