MolNFT v1 · #77369 · protein

Crystal structure of mandelate RACEMASE/MUCONATE lactonizing enzyme- like protein from roseovarius sp. TM1035

3RCY · Mandelate RACEMASE/MUCONATE lactonizing enzyme-like protein: “Crystal structure of mandelate RACEMASE/MUCONATE lactonizing enzyme- like protein from roseovarius sp. TM1035”. X-ray diffraction, 2 ligands (RIB, MG), 20 pockets (best…

PDB: 3RCY
Type: protein
Length: 3,166 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mandelate RACEMASE/MUCONATE lactonizing enzyme-like protein
UniProt: A6DZ31
Ligands: RIB, MG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, G	Mandelate RACEMASE/MUCONATE lactonizing enzyme-like protein	protein	396	40% helix, 15% strand	A6DZ31
B, E, H	Mandelate RACEMASE/MUCONATE lactonizing enzyme-like protein	protein	395	41% helix, 15% strand	A6DZ31
F	Mandelate RACEMASE/MUCONATE lactonizing enzyme-like protein	protein	397	40% helix, 15% strand	A6DZ31

Ligands and binding sites

RIB · alpha-D-ribofuranose · ligand · 8 copies · chains A, C, B, D, E, G, F, H
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
GOL · Glycerol · additive · 18 copies · chains A, E, D, B, F, H, C, G

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	498	0.85	0.92	77	RIB
2	527	0.85	0.91	78	RIB
3	453	0.85	0.92	74	RIB
4	549	0.85	0.91	78	RIB
5	805	0.84	0.87	105	GOL

Interfaces

16 interfaces between chains.

F–H · 2149 Å² buried · 45 hydrogen bonds · protein-protein
E–G · 2138 Å² buried · 46 hydrogen bonds · protein-protein
B–D · 2128 Å² buried · 44 hydrogen bonds · protein-protein
A–C · 2126 Å² buried · 43 hydrogen bonds · protein-protein
A–D · 1283 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

3RCY · CRYSTAL STRUCTURE OF Mandelate racemase/muconate lactonizing enzyme-like protein from… · 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 A6DZ31
Elsewhere: RCSB PDB 3RCY · PDBe 3RCY · UniProt A6DZ31

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