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Crystal structure of enolase superfamily member from vibrionales bacterium complexed with mg and glycerol in the active site

Analyse Crystal structure of enolase superfamily member from vibrionales bacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3R25
Type: protein
Length: 3,162 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mandelate racemase / muconate lactonizing enzyme
UniProt: A5KUH4
Ligands: MG
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 5 distinct chains · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Mandelate racemase / muconate lactonizing enzyme	protein	390	42% helix, 16% strand	A5KUH4
B, D, F	Mandelate racemase / muconate lactonizing enzyme	protein	399	42% helix, 17% strand	A5KUH4
E	Mandelate racemase / muconate lactonizing enzyme	protein	395	41% helix, 17% strand	A5KUH4
G	Mandelate racemase / muconate lactonizing enzyme	protein	395	40% helix, 17% strand	A5KUH4
H	Mandelate racemase / muconate lactonizing enzyme	protein	395	39% helix, 17% strand	A5KUH4

Ligands and binding sites

MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H
GOL · Glycerol · additive · 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	852	0.88	0.90	91	empty
2	855	0.87	0.90	90	empty
3	450	0.86	0.93	47	empty
4	423	0.86	0.94	50	empty
5	443	0.86	0.93	50	empty

Interfaces

16 interfaces between chains.

E–F · 2523 Å² buried · 29 hydrogen bonds · protein-protein
G–H · 2513 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 2488 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 2473 Å² buried · 36 hydrogen bonds · protein-protein
E–H · 1425 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

3R25 · Crystal structure of enolase superfamily member from Vibrionales bacterium complexed with… · the same entry in another collection · chain H against H, 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 3R25 · PDBe 3R25 · UniProt A5KUH4

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