MolNFT v1 · #46462 · protein

Crystal structure of a member of the enolase superfamily from salmonella typhimurium

2O56 · Putative mandelate racemase: “Crystal structure of a member of the enolase superfamily from salmonella typhimurium”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.84). MolNFT v1 #46462 on GenesisL1: 3D structure…

PDB: 2O56
Type: protein
Length: 3,132 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative mandelate racemase
UniProt: Q8ZKY6
Ligands: MG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Putative mandelate racemase	protein	392	42% helix, 16% strand	Q8ZKY6
G	Putative mandelate racemase	protein	391	42% helix, 17% strand	Q8ZKY6
H	Putative mandelate racemase	protein	389	42% helix, 17% strand	Q8ZKY6

Ligands and binding sites

MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	393	0.84	0.92	41	empty
2	399	0.84	0.92	41	empty
3	383	0.84	0.92	40	empty
4	1134	0.84	0.85	125	empty
5	102	0.79	0.99	22	empty

Interfaces

16 interfaces between chains.

C–G · 2037 Å² buried · 27 hydrogen bonds · protein-protein
F–H · 2035 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2022 Å² buried · 24 hydrogen bonds · protein-protein
D–E · 2018 Å² buried · 24 hydrogen bonds · protein-protein
D–G · 1381 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

2O56 · Crystal Structure of a Member of the Enolase Superfamily from Salmonella Typhimurium · 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 Q8ZKY6
Elsewhere: RCSB PDB 2O56 · PDBe 2O56 · UniProt Q8ZKY6

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