MolNFT v1 · #47764 · protein

Crystal structure of N-succinyl ARG/LYS racemase from bacillus cereus atcc 14579

2P88 · Mandelate RACEMASE/MUCONATE lactonizing enzyme family…: “Crystal structure of N-succinyl ARG/LYS racemase from bacillus cereus atcc 14579”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.87). MolNFT v1 #47764 on…

PDB: 2P88
Type: protein
Length: 2,952 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mandelate RACEMASE/MUCONATE lactonizing enzyme family protein
UniProt: Q81IL5
Ligands: MG
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Mandelate RACEMASE/MUCONATE lactonizing enzyme family protein	protein	369	40% helix, 24% strand	Q81IL5

Ligands and binding sites

MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	853	0.87	0.90	85	empty
2	475	0.85	0.92	78	empty
3	337	0.82	0.92	54	empty
4	346	0.82	0.92	48	empty
5	113	0.77	0.97	31	empty

Interfaces

16 interfaces between chains.

G–H · 1573 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 1566 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1552 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 1537 Å² buried · 22 hydrogen bonds · protein-protein
C–H · 1197 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

2P88 · Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579 · the same entry in another collection · chain H against H, TM-score 1.00
Q81IL5 · AlphaFold monomer V2.0 prediction for N-succinyl-L-ARG/LYS racemase (Q81IL5) · a predicted model of the same protein · 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 Q81IL5
Elsewhere: RCSB PDB 2P88 · PDBe 2P88 · UniProt Q81IL5

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