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Structure of deinococcus radiodurans N-acylamino acid racemase at 1.3 : insights into a flexible binding pocket and evolution of enzymatic activity

Analyse Structure of deinococcus radiodurans N-acylamino acid racemase at 1.3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1R0M
Type: protein
Length: 1,440 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N-acylamino acid racemase
UniProt: Q9RYA6
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	N-acylamino acid racemase	protein	360	36% helix, 23% strand	Q9RYA6

Pockets

7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	732	0.78	0.83	83	empty
2	746	0.78	0.82	77	empty
3	692	0.75	0.81	68	empty
4	74	0.62	0.90	18	empty
5	302	0.58	0.77	40	empty

Interfaces

3 interfaces between chains.

B–D · 1262 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1254 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 966 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

1R0M · Structure of Deinococcus radiodurans N-acylamino acid racemase at 1.3 : insights into a… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt Q9RYA6
Elsewhere: RCSB PDB 1R0M · PDBe 1R0M · UniProt Q9RYA6

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