MolNFT v1 · #119871 · protein
Crystal structure of beta-lactamase penp mutant-E166H in complex with cephaloridine as "pre-deacylation" intermediate
5GHZ: “Crystal structure of beta-lactamase penp mutant-E166H in complex with cephaloridine as "pre-deacylation"…”. X-ray diffraction, 1 ligand (CED), 4 pockets (best druggability 0.74). MolNFT v1 #119871 on GenesisL1: 3D structure, binding…
- PDB
- 5GHZ
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P00808
- Ligands
- CED
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Beta-lactamase (EC 3.5.2.6) | protein | 256 | 44% helix, 19% strand | P00808 |
Ligands and binding sites
- CED · 5-methyl-2-[2-oxo-1-(2-thiophen-2-yl-acetylamino)-ethyl]-3,6-dihydro-2H-[1,3]thiazine-4-carboxylic acid · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.74 | 0.77 | 104 | CED |
| 2 | 90 | 0.47 | 0.81 | 18 | empty |
| 3 | 76 | 0.47 | 0.82 | 19 | empty |
| 4 | 68 | 0.27 | 0.72 | 20 | CED |
Interfaces
1 interface between chains.
- B–A · 573 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5GHZ · Crystal structure of beta-lactamase PenP mutant-E166H in complex with cephaloridine as… · the same entry in another collection · chain B against B, TM-score 1.00
- P00808 · AlphaFold monomer V2.0 prediction for beta-lactamase (P00808) · 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 P00808
- Elsewhere: RCSB PDB 5GHZ · PDBe 5GHZ · UniProt P00808
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