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Crystal structure of family B DNA polymerase from hyperthermophilic archaeon pyrococcus kodakaraensis KOD1

Analyse Crystal structure of family B DNA polymerase from hyperthermophilic archaeon… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1WNS
Type: protein
Length: 729 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase
EC: 2.7.7.7
UniProt: P77933
Pockets: 12 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase (EC 2.7.7.7)	protein	729	38% helix, 18% strand	P77933

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	520	0.66	0.77	61	empty
2	260	0.60	0.79	32	empty
3	237	0.59	0.79	43	empty
4	194	0.57	0.80	22	empty
5	117	0.55	0.83	25	empty

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

1WNS · Crystal structure of family B DNA polymerase from hyperthermophilic archaeon pyrococcus… · the same entry in another collection · chain A against A, TM-score 1.00
P77933 · AlphaFold monomer V2.0 prediction for DNA polymerase (P77933) · a predicted model of the same protein · chain A against A, TM-score 0.85

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 P77933
Elsewhere: RCSB PDB 1WNS · PDBe 1WNS · UniProt P77933

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