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The crystal structure of alanine racemase from streptococcus pneumoniae

Analyse The crystal structure of alanine racemase from streptococcus pneumoniae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3S46
Type: protein
Length: 734 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alanine racemase
EC: 5.1.1.1
UniProt: P0A2W8
Ligands: BEZ
Pockets: 10 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alanine racemase (EC 5.1.1.1)	protein	367	33% helix, 26% strand	P0A2W8

Ligands and binding sites

BEZ · Benzoic acid · ligand · chains A

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

Pockets

10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	135	0.59	0.84	33	empty
2	124	0.59	0.85	32	empty
3	69	0.50	0.85	16	empty
4	88	0.44	0.80	20	empty
5	99	0.42	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 3223 Å² buried · 41 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (carboxylation, cofactor).

Compared structures

3S46 · The crystal structure of alanine racemase from streptococcus pneumoniae · the same entry in another collection · chain A against A, TM-score 1.00
P0A2W8 · AlphaFold monomer V2.0 prediction for alanine racemase (P0A2W8) · a predicted model of the same protein · 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 P0A2W8
Elsewhere: RCSB PDB 3S46 · PDBe 3S46 · UniProt P0A2W8

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