MolNFT v1 · #46726 · protein

Structure of a peptide derived from CDC9 bound to PCNA

2OD8 · Proliferating cell nuclear antigen: “Structure of a peptide derived from CDC9 bound to PCNA”. X-ray diffraction, 1 pocket (best druggability 0.60). MolNFT v1 #46726 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2OD8
Type: protein
Length: 266 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proliferating cell nuclear antigen; DNA ligase I, mitochondrial precursor
EC: 6.5.1.1
UniProt: P15873, P04819
Pockets: 1 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proliferating cell nuclear antigen	protein	255	18% helix, 45% strand	P15873
B	DNA ligase I, mitochondrial precursor (EC 6.5.1.1)	protein	11	36% helix, 18% strand	P04819

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	166	0.60	0.82	26	empty

Interfaces

1 interface between chains.

A–B · 628 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2OD8 · Structure of a peptide derived from Cdc9 bound to PCNA · the same entry in another collection · chain A against A, TM-score 1.00
P15873 · AlphaFold monomer V2.0 prediction for proliferating cell nuclear antigen (P15873) · a predicted model of the same protein · chain A against A, TM-score 0.98
P04819 · AlphaFold monomer V2.0 prediction for DNA ligase 1 (P04819) · a predicted model of the same protein · chain B against A, TM-score 0.38

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 P15873
Every structure of UniProt P04819
Elsewhere: RCSB PDB 2OD8 · PDBe 2OD8 · UniProt P15873 · UniProt P04819

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