MolNFT v1 · #96640 · protein
Structure of shv-1 beta-lactamase in complex with the 7- alkylidenecephalosporin dcm-1-10 at 1.14 ang resolution
4JPM · Beta-lactamase shv-1: “Structure of shv-1 beta-lactamase in complex with the 7- alkylidenecephalosporin dcm-1-10 at 1.14 ang…”. X-ray diffraction, 2 ligands (MA4, 1OG), 2 pockets (best druggability 0.69). MolNFT v1 #96640 on…
- PDB
- 4JPM
- Type
- protein
- Length
- 265 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase shv-1
- EC
- 3.5.2.6
- UniProt
- P0AD64
- Ligands
- MA4, 1OG
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase shv-1 (EC 3.5.2.6) | protein | 265 | 45% helix, 17% strand | P0AD64 |
Ligands and binding sites
- MA4 · Cyclohexyl-hexyl-beta-D-maltoside · ligand · 2 copies · chains A
- 1OG · 7-alkylidenecephalosporin DCM-1-10, bound form · ligand · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.69 | 0.86 | 23 | MA4 |
| 2 | 51 | 0.27 | 0.75 | 15 | 1OG, EPE |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 4JPM · Structure of SHV-1 beta-lactamase in complex with the 7-alkylidenecephalosporin DCM-1-10… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AD64 · AlphaFold monomer V2.0 prediction for beta-lactamase shv-1 (P0AD64) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0AD64
- Elsewhere: RCSB PDB 4JPM · PDBe 4JPM · UniProt P0AD64
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