Research workbench
Beta-lactamase, mixed with Ceftriaxone, 30ms time point, Shards crystal form
Analyse Beta-lactamase, mixed with Ceftriaxone, 30ms time point, Shards crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B5Y
- Type
- protein
- Length
- 1,060 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.75
- Source
- Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P9WKD3
- Ligands
- 9F2, PO4
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.75 · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 265 | 46% helix, 17% strand | P9WKD3 |
Ligands and binding sites
- 9F2 · Ceftriaxone · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.64 | 0.75 | 64 | 9F2 |
| 2 | 171 | 0.62 | 0.84 | 30 | PO4 |
| 3 | 152 | 0.61 | 0.85 | 31 | PO4 |
| 4 | 412 | 0.58 | 0.75 | 40 | 9F2 |
| 5 | 122 | 0.41 | 0.75 | 32 | empty |
Interfaces
4 interfaces between chains.
- C–D · 753 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 735 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 670 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 665 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6B5Y · Beta-lactamase, mixed with ceftriaxone, 30MS time point, shards crystal form · the same entry in another collection · chain D against D, TM-score 1.00
- P9WKD3 · AlphaFold monomer V2.0 prediction for beta-lactamase (P9WKD3) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P9WKD3
- Elsewhere: RCSB PDB 6B5Y · PDBe 6B5Y · UniProt P9WKD3
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