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Crystal structure of putative isomerase EC2056

Analyse Crystal structure of putative isomerase EC2056 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OTV
Type: protein
Length: 700 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative isomerase ybhh
EC: 5.-.-.-
UniProt: P0AAV8
Ligands: PO4
Pockets: 8 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Putative isomerase ybhh (EC 5.-.-.-)	protein	350	24% helix, 34% strand	P0AAV8

Ligands and binding sites

PO4 · Phosphate ion · ion · 4 copies · chains A, B
EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
ACT · Acetate ion · additive · 5 copies · chains A, B

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

Pockets

8 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	485	0.68	0.79	52	ACT, PO4
2	485	0.67	0.78	51	ACT, PO4
3	222	0.54	0.78	32	EDO
4	197	0.50	0.77	30	EDO
5	54	0.49	0.86	10	empty

Interfaces

1 interface between chains.

A–B · 895 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6OTV · Crystal structure of putative isomerase EC2056 · the same entry in another collection · chain A against A, TM-score 1.00
P0AAV8 · AlphaFold monomer V2.0 prediction for putative isomerase ybhh (P0AAV8) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P0AAV8
Elsewhere: RCSB PDB 6OTV · PDBe 6OTV · UniProt P0AAV8

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