MolNFT v1 · #100464 · protein

1.37 ångström crystal structure of E. COLI 2-succinyl-6-hydroxy-2,4- cyclohexadiene-1-carboxylate synthase (menh) in complex with shchc

4MYD · 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate…: “1.37 ångström crystal structure of E. COLI 2-succinyl-6-hydroxy-2,4- cyclohexadiene-1-carboxylate synthase…”. X-ray diffraction, 1 ligand (164), 6 pockets (best druggability…

PDB: 4MYD
Type: protein
Length: 754 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
EC: 4.2.99.20
UniProt: P37355
Ligands: 164
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (EC 4.2.99.20)	protein	252	46% helix, 15% strand	P37355
C	2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (EC 4.2.99.20)	protein	250	46% helix, 15% strand	P37355

Ligands and binding sites

164 · 2-(3-carboxypropionyl)-6-hydroxy-cyclohexa-2,4-diene carboxylic acid · ligand · 2 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	205	0.74	0.89	32	empty
2	220	0.72	0.87	32	164
3	261	0.69	0.84	33	164
4	383	0.59	0.76	74	empty
5	273	0.52	0.75	45	empty

Interfaces

2 interfaces between chains.

A–C · 619 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 362 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4MYD · 1.37 Angstrom Crystal Structure of E. Coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carbo… · the same entry in another collection · chain A against A, TM-score 1.00
P37355 · AlphaFold monomer V2.0 prediction for 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylat… · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P37355
Elsewhere: RCSB PDB 4MYD · PDBe 4MYD · UniProt P37355

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