MolNFT v1 · #78521 · protein

Crystal structure of the mutant P311A of enolase superfamily member from vibrionales bacterium complexed with mg and D-arabinonate

3SBF · Mandelate racemase / muconate lactonizing enzyme: “Crystal structure of the mutant P311A of enolase superfamily member from vibrionales bacterium complexed with…”. X-ray diffraction, 2 ligands (D8T, MG), 16 pockets (best…

PDB: 3SBF
Type: protein
Length: 1,583 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mandelate racemase / muconate lactonizing enzyme
UniProt: A5KUH4
Ligands: D8T, MG
Pockets: 16 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Mandelate racemase / muconate lactonizing enzyme	protein	397	41% helix, 17% strand	A5KUH4
B	Mandelate racemase / muconate lactonizing enzyme	protein	390	41% helix, 17% strand	A5KUH4
D	Mandelate racemase / muconate lactonizing enzyme	protein	399	41% helix, 17% strand	A5KUH4

Ligands and binding sites

D8T · D-arabinonic acid · ligand · 4 copies · chains A, D, B, C
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, C

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

Pockets

16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	734	0.88	0.92	85	empty
2	696	0.87	0.91	84	empty
3	61	0.73	0.99	19	empty
4	389	0.67	0.81	50	empty
5	486	0.66	0.78	41	EPE, D8T

Interfaces

5 interfaces between chains.

B–C · 2570 Å² buried · 37 hydrogen bonds · protein-protein
A–D · 2561 Å² buried · 38 hydrogen bonds · protein-protein
A–B · 1312 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 1293 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 1277 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

3SBF · Crystal structure of the mutant P311A of enolase superfamily member from VIBRIONALES… · the same entry in another collection · chain A against A, TM-score 1.00
A5KUH4 · AlphaFold monomer V2.0 prediction for D-galactonate dehydratase family member… · 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 A5KUH4
Elsewhere: RCSB PDB 3SBF · PDBe 3SBF · UniProt A5KUH4

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