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Alpha-amino epsilon-caprolactam racemase K241A mutant in complex with D-acl (external aldimine)

Analyse Alpha-amino epsilon-caprolactam racemase K241A mutant in complex with D-acl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5M4D
Type: protein
Length: 439 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminotransferase class-III
UniProt: N6UXY4
Ligands: 7F7
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aminotransferase class-III	protein	439	41% helix, 18% strand	N6UXY4

Ligands and binding sites

7F7 · [6-methyl-5-oxidanyl-4-[(~{E})-[(3~{R})-2-oxidanylideneazepan-3-yl]iminomethyl]pyridin-3-yl]methyl dihydrogen phosphate · ligand · chains A
EDO · 1,2-ethanediol · additive · 4 copies · chains A

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

Pockets

3 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	451	0.61	0.75	49	7F7
2	216	0.57	0.79	30	empty
3	110	0.46	0.79	22	empty

Compared structures

5M4D · Alpha-amino epsilon-caprolactam racemase K241A mutant in complex with D-ACL (external… · the same entry in another collection · 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 N6UXY4
Elsewhere: RCSB PDB 5M4D · PDBe 5M4D · UniProt N6UXY4

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