MolNFT v1 · #117803 · protein

Ecmend-thdp-MN2+ complex soaked with 2-ketoglutarate for 1.5 H

5EJ5 · 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1…: “Ecmend-thdp-MN2+ complex soaked with 2-ketoglutarate for 1.5 H”. X-ray diffraction, 2 ligands (TD6, MN), 20 pockets (best druggability 0.86). MolNFT v1 #117803 on GenesisL1: 3D…

PDB: 5EJ5
Type: protein
Length: 4,448 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase
EC: 2.2.1.9
UniProt: P17109
Ligands: TD6, MN
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9)	protein	556	42% helix, 16% strand	P17109

Ligands and binding sites

TD6 · (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
MN · Manganese (II) ion · metal · 8 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	681	0.86	0.90	110	TD6, MN
2	603	0.85	0.90	98	TD6, MN
3	600	0.85	0.90	98	TD6, MN
4	818	0.84	0.87	134	empty
5	941	0.82	0.83	115	TD6, MN

Interfaces

15 interfaces between chains.

A–B · 3528 Å² buried · 50 hydrogen bonds · protein-protein
E–F · 3523 Å² buried · 50 hydrogen bonds · protein-protein
C–D · 3518 Å² buried · 52 hydrogen bonds · protein-protein
G–H · 3494 Å² buried · 52 hydrogen bonds · protein-protein
B–D · 1577 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

5EJ5 · EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 1.5 h · the same entry in another collection · chain H against H, TM-score 1.00
P17109 · AlphaFold monomer V2.0 prediction for 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-c… · a predicted model of the same protein · chain A 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 P17109
Elsewhere: RCSB PDB 5EJ5 · PDBe 5EJ5 · UniProt P17109

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