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Crystal structure of vibrio parahaemolyticus yeaz

Analyse Crystal structure of vibrio parahaemolyticus yeaz in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3R6M
Type: protein
Length: 848 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yeaz, resuscitation promoting factor
UniProt: Q87RD1
Pockets: 12 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Yeaz, resuscitation promoting factor	protein	212	31% helix, 30% strand	Q87RD1

Pockets

12 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	381	0.71	0.83	56	empty
2	649	0.68	0.76	76	empty
3	632	0.67	0.76	71	empty
4	84	0.56	0.86	23	empty
5	232	0.50	0.75	30	empty

Interfaces

5 interfaces between chains.

A–B · 1034 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 941 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 937 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 168 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 166 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3R6M · Crystal structure of Vibrio parahaemolyticus YeaZ · the same entry in another collection · chain B against B, TM-score 1.00
Q87RD1 · AlphaFold monomer V2.0 prediction for tRNA threonylcarbamoyladenosine biosynthesis… · a predicted model of the same protein · chain A against A, TM-score 0.98

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q87RD1
Elsewhere: RCSB PDB 3R6M · PDBe 3R6M · UniProt Q87RD1

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