MolNFT v1 · #110569 · protein
Crystal structure of apo form of oxa-58, a carbapenem hydrolyzing class D beta-lactamase from acinetobacter baumanii (P21, 4MOL/ASU)
4Y0T: “Crystal structure of apo form of oxa-58, a carbapenem hydrolyzing class D beta-lactamase from acinetobacter…”. X-ray diffraction, 8 pockets (best druggability 0.73). MolNFT v1 #110569 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4Y0T
- Type
- protein
- Length
- 968 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q2TR58
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 42% helix, 21% strand | Q2TR58 |
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.73 | 0.78 | 79 | empty |
| 2 | 420 | 0.65 | 0.78 | 55 | empty |
| 3 | 278 | 0.53 | 0.75 | 30 | empty |
| 4 | 241 | 0.53 | 0.76 | 28 | empty |
| 5 | 245 | 0.51 | 0.75 | 29 | empty |
Interfaces
4 interfaces between chains.
- B–C · 358 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 329 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 208 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 122 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 4Y0T · Crystal structure of apo form of OXA-58, a Carbapenem hydrolyzing Class D beta-lactamase… · the same entry in another collection · 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 Q2TR58
- Elsewhere: RCSB PDB 4Y0T · PDBe 4Y0T · UniProt Q2TR58
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.