MolNFT v1 · #92630 · protein

Crystal structure of E.COLI menh R124A mutant

4GEC · 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate…: “Crystal structure of E.COLI menh R124A mutant”. X-ray diffraction, 2 ligands (SO4, CL), 9 pockets (best druggability 0.73). MolNFT v1 #92630 on GenesisL1: 3D structure…

PDB: 4GEC
Type: protein
Length: 769 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: SO4, CL
Pockets: 9 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (EC 4.2.99.20)	protein	257	46% helix, 15% strand	P37355
B	2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (EC 4.2.99.20)	protein	253	45% helix, 15% strand	P37355
C	2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (EC 4.2.99.20)	protein	259	46% helix, 15% strand	P37355

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, C, B
CL · Chloride ion · ion · 3 copies · chains A, B, C
GOL · Glycerol · additive · chains A
EDO · 1,2-ethanediol · additive · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	285	0.73	0.86	35	SO4, CL
2	617	0.72	0.80	59	SO4
3	297	0.72	0.85	36	SO4
4	295	0.72	0.85	32	SO4
5	90	0.38	0.76	26	CL

Interfaces

3 interfaces between chains.

B–C · 893 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 548 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 264 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4GEC · Crystal Structure of E.coli MenH R124A Mutant · 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 B 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 4GEC · PDBe 4GEC · UniProt P37355

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