MolNFT v1 · #78200 · protein
AMP-C beta-lactamase (pseudomonas aeruginosa) in complex with a beta- lactamase inhibitor
3S1Y: “AMP-C beta-lactamase (pseudomonas aeruginosa) in complex with a beta- lactamase inhibitor”. X-ray diffraction, 2 ligands (S1Y, CL), 2 pockets (best druggability 0.60). MolNFT v1 #78200 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3S1Y
- Type
- protein
- Length
- 361 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P24735
- Ligands
- S1Y, CL
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 361 | 43% helix, 22% strand | P24735 |
Ligands and binding sites
- S1Y · [(2S,3R)-1-{[(4S)-1-(2-aminoethyl)azepan-4-yl]carbamoyl}-2-formylpyrrolidin-3-yl]sulfamic acid · ligand · chains A
- CL · Chloride ion · ion · chains A
- IPA · Isopropyl alcohol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.60 | 0.80 | 39 | S1Y, CL, IPA |
| 2 | 65 | 0.31 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3S1Y · AMP-C BETA-LACTAMASE (PSEUDOMONAS AERUGINOSA) in complex with a beta-lactamase inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P24735 · AlphaFold monomer V2.0 prediction for beta-lactamase (P24735) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P24735
- Elsewhere: RCSB PDB 3S1Y · PDBe 3S1Y · UniProt P24735
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