MolNFT v1 · #52733 · protein

Structure of family X DNA polymerase from deinococcus radiodurans

2W9M · Polymerase X: “Structure of family X DNA polymerase from deinococcus radiodurans”. X-ray diffraction, 2 ligands (ZN, HG), 13 pockets (best druggability 0.78). MolNFT v1 #52733 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2W9M
Type: protein
Length: 1,100 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polymerase X
UniProt: Q9RX48
Ligands: ZN, HG
Pockets: 13 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polymerase X	protein	541	48% helix, 15% strand	Q9RX48
B	Polymerase X	protein	559	47% helix, 14% strand	Q9RX48

Ligands and binding sites

ZN · Zinc ion · metal · 7 copies · chains A, B
HG · Mercury (II) ion · metal · 2 copies · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1142	0.78	0.80	113	empty
2	1046	0.72	0.76	71	empty
3	92	0.64	0.90	29	empty
4	91	0.59	0.87	33	empty
5	154	0.45	0.76	27	empty

Interfaces

1 interface between chains.

A–B · 1183 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

2W9M · Structure of family X DNA polymerase from Deinococcus radiodurans · the same entry in another collection · chain A against A, TM-score 1.00

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 Q9RX48
Elsewhere: RCSB PDB 2W9M · PDBe 2W9M · UniProt Q9RX48

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