Research workbench
Crystal structure of P99 beta-lactamase in complex with a penicillin derivative mpc-1
Analyse Crystal structure of P99 beta-lactamase in complex with a penicillin derivative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XHR
- Type
- protein
- Length
- 359 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P05364
- Ligands
- PXH
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 359 | 40% helix, 23% strand | P05364 |
Ligands and binding sites
- PXH · (2~{R},4~{S})-5,5-dimethyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-5-thiophen-2-yl-pentan-2-yl]-1,3-thiazolidine-4-carboxylic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.61 | 0.80 | 40 | PXH |
| 2 | 78 | 0.32 | 0.73 | 21 | empty |
| 3 | 58 | 0.28 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5XHR · Crystal structure of P99 beta-lactamase in complex with a penicillin derivative MPC-1 · the same entry in another collection · chain A against A, TM-score 1.00
- P05364 · AlphaFold monomer V2.0 prediction for beta-lactamase (P05364) · 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 P05364
- Elsewhere: RCSB PDB 5XHR · PDBe 5XHR · UniProt P05364
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