MolNFT v1 · #119023 · protein

Structure of L-amino acid deaminase from proteus myxofaciens

5FJM: “Structure of L-amino acid deaminase from proteus myxofaciens”. X-ray diffraction, 1 ligand (FAD), 6 pockets (best druggability 0.82). MolNFT v1 #119023 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5FJM
Type: protein
Length: 894 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-amino acid deaminase
Ligands: FAD
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	L-amino acid deaminase	protein	447	32% helix, 24% strand	—

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B

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

Pockets

6 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	994	0.82	0.83	93	FAD
2	1016	0.81	0.82	90	FAD
3	1106	0.80	0.82	97	empty
4	285	0.75	0.88	33	empty
5	254	0.73	0.87	37	empty

Interfaces

1 interface between chains.

A–B · 751 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5FJM · Structure of L-Amino acid deaminase from Proteus myxofaciens · 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
Elsewhere: RCSB PDB 5FJM · PDBe 5FJM

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