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Structure of amino acid racemase, 2.65 a

Analyse Structure of amino acid racemase, 2.65 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WYA
Type: protein
Length: 1,758 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isoleucine 2-epimerase
EC: 5.1.1.21
UniProt: M1GRN3
Ligands: 7VO
Pockets: 12 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Isoleucine 2-epimerase (EC 5.1.1.21)	protein	439	42% helix, 18% strand	M1GRN3
B, C	Isoleucine 2-epimerase (EC 5.1.1.21)	protein	440	42% helix, 18% strand	M1GRN3

Ligands and binding sites

7VO · (2S,3S)-3-methyl-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pentanoic acid · ligand · 4 copies · chains A, B, C, D
DMS · Dimethyl sulfoxide · additive · 11 copies · chains A, C, D, B

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	259	0.85	0.96	45	empty
2	249	0.84	0.95	42	empty
3	686	0.77	0.82	65	7VO
4	628	0.76	0.82	67	7VO
5	627	0.76	0.82	68	7VO

Interfaces

6 interfaces between chains.

C–D · 5294 Å² buried · 85 hydrogen bonds · protein-protein
A–B · 5251 Å² buried · 79 hydrogen bonds · protein-protein
A–D · 1312 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1301 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 99 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5WYA · Structure of amino acid racemase, 2.65 A · the same entry in another collection · chain D against D, TM-score 1.00
M1GRN3 · AlphaFold monomer V2.0 prediction for isoleucine 2-epimerase (M1GRN3) · 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 M1GRN3
Elsewhere: RCSB PDB 5WYA · PDBe 5WYA · UniProt M1GRN3

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