MolNFT v1 · #138911 · protein

Structure of amino acid racemase, 2.12 a

5WYF · Isoleucine 2-epimerase: “Structure of amino acid racemase, 2.12 a”. X-ray diffraction, 2 ligands (ILP, CD), 18 pockets (best druggability 0.84). MolNFT v1 #138911 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5WYF
Type: protein
Length: 1,780 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: ILP, CD
Pockets: 18 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Isoleucine 2-epimerase (EC 5.1.1.21)	protein	446	41% helix, 18% strand	M1GRN3
B, D	Isoleucine 2-epimerase (EC 5.1.1.21)	protein	444	41% helix, 18% strand	M1GRN3

Ligands and binding sites

ILP · N-[O-phosphono-pyridoxyl]-isoleucine · ligand · 4 copies · chains A, B, C, D
CD · Cadmium ion · metal · 36 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	245	0.84	0.96	44	empty
2	226	0.83	0.96	44	empty
3	129	0.81	0.99	37	ILP
4	124	0.80	0.98	34	ILP
5	118	0.79	0.98	31	ILP

Interfaces

6 interfaces between chains.

C–D · 5209 Å² buried · 88 hydrogen bonds · protein-protein
A–B · 5186 Å² buried · 88 hydrogen bonds · protein-protein
B–D · 1309 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 1303 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 88 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5WYF · Structure of amino acid racemase, 2.12 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 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 M1GRN3
Elsewhere: RCSB PDB 5WYF · PDBe 5WYF · UniProt M1GRN3

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