MolNFT v1 · #24961 · protein

Crystal structure of PH1313 from pyrococcus horikoshii OT3

1VBK · Hypothetical protein PH1313: “Crystal structure of PH1313 from pyrococcus horikoshii OT3”. X-ray diffraction, 5 pockets (best druggability 0.74). MolNFT v1 #24961 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VBK
Type: protein
Length: 603 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein PH1313
UniProt: O59053
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein PH1313	protein	307	40% helix, 24% strand	O59053
B	Hypothetical protein PH1313	protein	296	40% helix, 25% strand	O59053

Ligands and binding sites

MRD · (4R)-2-methylpentane-2,4-diol · additive · 4 copies · chains A, B

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

Pockets

5 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	648	0.74	0.81	61	empty
2	111	0.46	0.78	13	MRD
3	95	0.45	0.78	13	MRD
4	51	0.32	0.77	11	empty
5	50	0.24	0.73	18	empty

Interfaces

1 interface between chains.

A–B · 747 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1VBK · Crystal structure of PH1313 from Pyrococcus horikoshii Ot3 · 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 O59053
Elsewhere: RCSB PDB 1VBK · PDBe 1VBK · UniProt O59053

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