MolNFT v1 · #35592 · protein

The crystal structure of D-amino acid amidase from ochrobactrum anthropi SV3 complexed with L-phenylalanine amide

2EFX: “The crystal structure of D-amino acid amidase from ochrobactrum anthropi SV3 complexed with L-phenylalanine…”. X-ray diffraction, 2 ligands (NFA, BA), 20 pockets (best druggability 0.85). MolNFT v1 #35592 on GenesisL1: 3D structure…

PDB: 2EFX
Type: protein
Length: 2,073 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-amino acid amidase
UniProt: Q9LCC8
Ligands: NFA, BA
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 36% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	D-amino acid amidase	protein	362	35% helix, 22% strand	Q9LCC8
C	D-amino acid amidase	protein	358	34% helix, 22% strand	Q9LCC8
D	D-amino acid amidase	protein	350	37% helix, 21% strand	Q9LCC8
E	D-amino acid amidase	protein	345	37% helix, 20% strand	Q9LCC8
F	D-amino acid amidase	protein	296	34% helix, 13% strand	Q9LCC8

Ligands and binding sites

NFA · Phenylalanine amide · ligand · 6 copies · chains A, B, C, D, E, F
BA · Barium ion · metal · 22 copies · chains A, D, B, F, C, E

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	801	0.85	0.88	87	BA
2	769	0.84	0.87	71	BA
3	332	0.74	0.86	46	empty
4	216	0.74	0.89	31	NFA
5	302	0.70	0.84	46	NFA

Interfaces

9 interfaces between chains.

D–E · 548 Å² buried · 4 hydrogen bonds · protein-protein
B–F · 539 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 502 Å² buried · 4 hydrogen bonds · protein-protein
C–E · 494 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 478 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2EFX · The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed… · 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 Q9LCC8
Elsewhere: RCSB PDB 2EFX · PDBe 2EFX · UniProt Q9LCC8

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