MolNFT v1 · #12912 · protein
X-ray crystal structure of ampc wt beta-lactamase in complex with covalently bound cephalothin
1KVM: “X-ray crystal structure of ampc wt beta-lactamase in complex with covalently bound cephalothin”. X-ray diffraction, 2 ligands (CEO, PO4), 8 pockets (best druggability 0.79). MolNFT v1 #12912 on GenesisL1: 3D structure, binding sites…
- PDB
- 1KVM
- Type
- protein
- Length
- 712 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P00811
- Ligands
- CEO, PO4
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 354 | 38% helix, 23% strand | P00811 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 41% helix, 23% strand | P00811 |
Ligands and binding sites
- CEO · 5-methylene-2-[2-oxo-1-(2-thiophen-2-yl-acetylamino)-ethyl]-5,6-dihydro-2H-[1,3]thiazine-4-carboxylic acid · ligand · chains B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.79 | 0.89 | 60 | empty |
| 2 | 419 | 0.70 | 0.81 | 53 | empty |
| 3 | 320 | 0.66 | 0.81 | 56 | CEO |
| 4 | 150 | 0.48 | 0.77 | 39 | empty |
| 5 | 65 | 0.47 | 0.84 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 742 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1KVM · X-ray Crystal Structure of AmpC WT beta-Lactamase in Complex with Covalently Bound… · the same entry in another collection · chain B against B, TM-score 1.00
- 1L2S · X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with a… · a predicted model of the same protein · chain B against B, TM-score 1.00
- P00811 · AlphaFold monomer V2.0 prediction for beta-lactamase (P00811) · a predicted model of the same protein · chain B 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 P00811
- Elsewhere: RCSB PDB 1KVM · PDBe 1KVM · UniProt P00811
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