Research workbench
Crystal structure of 6ALPHA-hydroxymethylpenicillanate complexed with oxa-58, a carbapenem hydrolyzing class D betalactamase from acinetobacter baumanii.
Analyse Crystal structure of 6ALPHA-hydroxymethylpenicillanate complexed with oxa-58, a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y0U
- Type
- protein
- Length
- 971 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
- Ligands
- ALP
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 243 | 41% helix, 21% strand | Q2TR58 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 41% helix, 21% strand | Q2TR58 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 243 | 42% helix, 21% strand | Q2TR58 |
Ligands and binding sites
- ALP · 2-(1-carboxy-2-hydroxy-ethyl)-5,5-dimethyl-thiazolidine-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 845 | 0.74 | 0.79 | 77 | empty |
| 2 | 667 | 0.70 | 0.77 | 74 | empty |
| 3 | 248 | 0.55 | 0.77 | 33 | ALP |
| 4 | 245 | 0.54 | 0.76 | 35 | ALP |
| 5 | 236 | 0.53 | 0.76 | 36 | ALP |
Interfaces
4 interfaces between chains.
- B–C · 371 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 337 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 212 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 153 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, carboxylation).
Compared structures
- 4Y0U · Crystal Structure of 6Alpha-Hydroxymethylpenicillanate Complexed with OXA-58, a… · 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 4Y0U · PDBe 4Y0U · UniProt Q2TR58
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