Research workbench

Alanine racemase bound with N-(5'-phosphopyridoxyl)-D- alanine

Analyse Alanine racemase bound with N-(5'-phosphopyridoxyl)-D- alanine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1L6G
Type: protein
Length: 764 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alanine racemase
EC: 5.1.1.1
UniProt: P10724
Ligands: PDD
Pockets: 9 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alanine racemase (EC 5.1.1.1)	protein	382	33% helix, 27% strand	P10724

Ligands and binding sites

PDD · N-(5'-phosphopyridoxyl)-D-alanine · ligand · 2 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	221	0.76	0.90	49	PDD
2	234	0.76	0.90	54	PDD
3	437	0.72	0.82	72	empty
4	94	0.53	0.84	21	empty
5	99	0.51	0.82	21	empty

Interfaces

1 interface between chains.

A–B · 3336 Å² buried · 55 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (carboxylation).

Compared structures

1L6G · Alanine racemase bound with N-(5'-phosphopyridoxyl)-D-alanine · the same entry in another collection · chain A against A, TM-score 1.00
P10724 · AlphaFold monomer V2.0 prediction for alanine racemase (P10724) · a predicted model of the same protein · chain B 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 P10724
Elsewhere: RCSB PDB 1L6G · PDBe 1L6G · UniProt P10724

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