MolNFT v1 · #172881 · protein

Bsrv no-histagged

7AGZ · Broad specificity amino-acid racemase: “Bsrv no-histagged”. X-ray diffraction, 2 ligands (PLP, CL), 8 pockets (best druggability 0.79). MolNFT v1 #172881 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7AGZ
Type: protein
Length: 774 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Broad specificity amino-acid racemase
EC: 5.1.1.10
UniProt: Q9KSE5
Ligands: PLP, CL
Pockets: 8 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Broad specificity amino-acid racemase (EC 5.1.1.10)	protein	386	36% helix, 24% strand	Q9KSE5
B	Broad specificity amino-acid racemase (EC 5.1.1.10)	protein	388	36% helix, 24% strand	Q9KSE5

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 2 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	428	0.79	0.87	65	empty
2	311	0.78	0.89	54	PLP, GOL, CL
3	86	0.77	0.98	25	empty
4	272	0.76	0.88	47	PLP, GOL
5	50	0.45	0.85	19	empty

Interfaces

1 interface between chains.

A–B · 3386 Å² buried · 56 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor, 2 disulfide (pyridoxal phosphate Schiff base, disulfide).

Compared structures

7AGZ · BsrV no-histagged · the same entry in another collection · chain A against A, TM-score 1.00
Q9KSE5 · AlphaFold monomer V2.0 prediction for broad specificity amino-acid racemase (Q9KSE5) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9KSE5
Elsewhere: RCSB PDB 7AGZ · PDBe 7AGZ · UniProt Q9KSE5

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