MolNFT v1 · #164748 · protein

Structure of PCNA bound to cpip motif of DP2 from P. abyssi

6T7Y · DNA polymerase sliding clamp: “Structure of PCNA bound to cpip motif of DP2 from P. abyssi”. X-ray diffraction, 3 pockets (best druggability 0.74). MolNFT v1 #164748 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6T7Y
Type: protein
Length: 247 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase sliding clamp; Cpip motif from the DP2 large subunit of pold
EC: 2.7.7.7
UniProt: Q9UYX8
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase sliding clamp	protein	238	18% helix, 48% strand	Q9UYX8
B	Cpip motif from the DP2 large subunit of pold (EC 2.7.7.7)	protein	9	0% helix, 11% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	56	0.74	0.99	20	empty
2	130	0.43	0.76	22	empty
3	69	0.30	0.74	24	empty

Interfaces

1 interface between chains.

A–B · 491 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6T7Y · Structure of PCNA bound to cPIP motif of DP2 from P. abyssi · the same entry in another collection · chain A against A, TM-score 1.00
Q9UYX8 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp (Q9UYX8) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9UYX8
Elsewhere: RCSB PDB 6T7Y · PDBe 6T7Y · UniProt Q9UYX8

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