MolNFT v1 · #20510 · protein
Citrobacter freundii GN346 class C beta-lactamase complexed with transition-state analog of cefotaxime
1RGY: “Citrobacter freundii GN346 class C beta-lactamase complexed with transition-state analog of cefotaxime”. X-ray diffraction, 1 ligand (PTX), 2 pockets (best druggability 0.62). MolNFT v1 #20510 on GenesisL1: 3D structure, binding…
- PDB
- 1RGY
- Type
- protein
- Length
- 360 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P05193
- Ligands
- PTX
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 360 | 39% helix, 23% strand | P05193 |
Ligands and binding sites
- PTX · {[(2E)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)ethanoyl]amino}methylphosphonic acid · ligand · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · 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 | 298 | 0.62 | 0.80 | 42 | PTX |
| 2 | 99 | 0.35 | 0.74 | 18 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1RGY · Citrobacter freundii GN346 Class C beta-Lactamase Complexed with Transition-State Analog… · the same entry in another collection · chain A against A, TM-score 1.00
- P05193 · AlphaFold monomer V2.0 prediction for beta-lactamase (P05193) · 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 P05193
- Elsewhere: RCSB PDB 1RGY · PDBe 1RGY · UniProt P05193
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