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X-ray crystal structure of the heterodimeric complex of XRCC1 and DNA ligase III-alpha brct domains.

Analyse X-ray crystal structure of the heterodimeric complex of XRCC1 and DNA ligase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PC8
Type: protein
Length: 348 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair protein XRCC1; DNA ligase 3
EC: 6.5.1.1
UniProt: Q60596, P49916
Ligands: MG
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA repair protein XRCC1	protein	97	35% helix, 15% strand	Q60596
B	DNA repair protein XRCC1	protein	96	35% helix, 16% strand	Q60596
C	DNA ligase 3 (EC 6.5.1.1)	protein	77	34% helix, 14% strand	P49916
D	DNA ligase 3 (EC 6.5.1.1)	protein	78	29% helix, 14% strand	P49916

Ligands and binding sites

MG · Magnesium ion · metal · chains B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	211	0.67	0.85	34	empty
2	241	0.52	0.76	30	empty
3	176	0.43	0.73	27	TRS

Interfaces

3 interfaces between chains.

A–C · 650 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 630 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 507 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3PC8 · X-ray crystal structure of the heterodimeric complex of XRCC1 and DNA ligase III-alpha… · the same entry in another collection · chain D against D, TM-score 1.00
Q60596 · AlphaFold monomer V2.0 prediction for DNA repair protein XRCC1 (Q60596) · a predicted model of the same protein · chain B against A, TM-score 0.96
P49916 · AlphaFold monomer V2.0 prediction for DNA ligase 3 (P49916) · a predicted model of the same protein · chain C against A, TM-score 0.94

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q60596
Every structure of UniProt P49916
Elsewhere: RCSB PDB 3PC8 · PDBe 3PC8 · UniProt Q60596 · UniProt P49916

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