GL1X · GenesisL1 explorer

MolNFT v1 · #114965 · protein

R195K E. COLI mene with bound osb-ams

5C5H · 2-succinylbenzoate--CoA ligase: “R195K E. COLI mene with bound osb-ams”. X-ray diffraction, 2 ligands (4YB, MG), 6 pockets (best druggability 0.84). MolNFT v1 #114965 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
5C5H
Type
protein
Length
891 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
2-succinylbenzoate--CoA ligase
EC
6.2.1.26
UniProt
P37353
Ligands
4YB, MG
Pockets
6 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 30% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A2-succinylbenzoate--CoA ligase (EC 6.2.1.26)protein44328% helix, 30% strandP37353
B2-succinylbenzoate--CoA ligase (EC 6.2.1.26)protein44829% helix, 30% strandP37353

Ligands and binding sites

  • 4YB · 5'-O-{[4-(2-carboxyphenyl)-4-oxobutanoyl]sulfamoyl}adenosine · ligand · 2 copies · chains A, B
  • MG · Magnesium ion · metal · 3 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, 3 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
111310.840.85106MG, 4YB
211380.810.82974YB
34320.610.7647empty
41160.390.7518empty
5530.320.7611empty

Interfaces

1 interface between chains.

  • A–B · 364 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

  • 5C5H · R195K E. coli MenE with bound OSB-AMS · the same entry in another collection · chain A against A, TM-score 1.00
  • P37353 · AlphaFold monomer V2.0 prediction for 2-succinylbenzoate--CoA ligase (P37353) · a predicted model of the same protein · chain B against A, TM-score 1.00

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.