MolNFT v1 · #118223 · protein
Crystal structure of the metallo-beta-lactamase L1 in complex with the bisthiazolidine inhibitor D-VC26
5EVD: “Crystal structure of the metallo-beta-lactamase L1 in complex with the bisthiazolidine inhibitor D-VC26”. X-ray diffraction, 3 ligands (VC2, ZN, SO4), 2 pockets (best druggability 0.44). MolNFT v1 #118223 on GenesisL1: 3D structure…
- PDB
- 5EVD
- Type
- protein
- Length
- 267 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
- VC2, ZN, SO4
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase L1 (EC 3.5.2.6) | protein | 267 | 31% helix, 24% strand | P52700 |
Ligands and binding sites
- VC2 · (3S,5S,7aR)-2,2-dimethyl-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.44 | 0.76 | 28 | VC2, ZN |
| 2 | 63 | 0.31 | 0.75 | 21 | SO4 |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5EVD · Crystal structure of the metallo-beta-lactamase L1 in complex with the bisthiazolidine… · 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
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 P52700
- Elsewhere: RCSB PDB 5EVD · PDBe 5EVD · UniProt P52700
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