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MolNFT v1 · #120969 · protein

Crystal structure of B3 metallo-beta-lactamase L1 complexed with a phosphonate-based inhibitor

5HH5: “Crystal structure of B3 metallo-beta-lactamase L1 complexed with a phosphonate-based inhibitor”. X-ray diffraction, 3 ligands (60M, ZN, SO4), 2 pockets (best druggability 0.43). MolNFT v1 #120969 on GenesisL1: 3D structure, binding…

PDB
5HH5
Type
protein
Length
266 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Metallo-beta-lactamase L1
EC
3.5.2.6
UniProt
P52700
Ligands
60M, ZN, SO4
Pockets
2 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AMetallo-beta-lactamase L1 (EC 3.5.2.6)protein26630% helix, 24% strandP52700

Ligands and binding sites

  • 60M · 6-(phosphonomethyl)pyridine-2-carboxylic acid · ligand · chains A
  • ZN · Zinc ion · metal · chains A
  • SO4 · Sulfate ion · ion · 4 copies · chains A
  • GOL · Glycerol · additive · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11190.430.7726ZN, 60M
2550.280.7420SO4

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

  • 5HH5 · Crystal structure of B3 metallo-beta-lactamase L1 complexed with a phosphonate-based… · the same entry in another collection · chain A against A, TM-score 1.00
  • P52700 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase L1 type 3 (P52700) · a predicted model of the same protein · chain A against A, TM-score 1.00

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