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Crystal structure of mandelate RACEMASE/MUCONATE lactonizing enzyme from a marine actinobacterium in complex with magnesium

Analyse Crystal structure of mandelate RACEMASE/MUCONATE lactonizing enzyme from a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NO1
Type: protein
Length: 2,113 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mandelate RACEMASE/MUCONATE lactonizing enzyme
UniProt: A4AFX2
Ligands: MG
Pockets: 15 · best druggability 0.87

Structure

x-ray diffraction · 6 distinct chains · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mandelate RACEMASE/MUCONATE lactonizing enzyme	protein	355	42% helix, 21% strand	A4AFX2
B	Mandelate RACEMASE/MUCONATE lactonizing enzyme	protein	349	41% helix, 20% strand	A4AFX2
C	Mandelate RACEMASE/MUCONATE lactonizing enzyme	protein	357	42% helix, 20% strand	A4AFX2
D	Mandelate RACEMASE/MUCONATE lactonizing enzyme	protein	350	41% helix, 20% strand	A4AFX2
E	Mandelate RACEMASE/MUCONATE lactonizing enzyme	protein	353	42% helix, 20% strand	A4AFX2
F	Mandelate RACEMASE/MUCONATE lactonizing enzyme	protein	349	42% helix, 20% strand	A4AFX2

Ligands and binding sites

MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	352	0.87	0.96	41	empty
2	334	0.86	0.95	40	empty
3	352	0.86	0.95	38	empty
4	1088	0.85	0.86	101	empty
5	1027	0.84	0.85	98	empty

Interfaces

12 interfaces between chains.

E–F · 1230 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1211 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1202 Å² buried · 14 hydrogen bonds · protein-protein
A–E · 1123 Å² buried · 15 hydrogen bonds · protein-protein
C–F · 1117 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 60 modified (engineered).

Compared structures

3NO1 · Crystal Structure of Mandelate racemase/muconate lactonizing enzyme from a Marine… · 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 A4AFX2
Elsewhere: RCSB PDB 3NO1 · PDBe 3NO1 · UniProt A4AFX2

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