MolNFT v1 · #143651 · protein
Beta-lactamase, unmixed shards crystal form
6B5X: “Beta-lactamase, unmixed shards crystal form”. X-ray diffraction, 1 ligand (PO4), 10 pockets (best druggability 0.64). MolNFT v1 #143651 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6B5X
- Type
- protein
- Length
- 1,060 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P9WKD3
- Ligands
- PO4
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 265 | 45% helix, 16% strand | P9WKD3 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.64 | 0.84 | 34 | PO4 |
| 2 | 545 | 0.64 | 0.76 | 45 | PO4 |
| 3 | 149 | 0.61 | 0.85 | 27 | PO4 |
| 4 | 449 | 0.61 | 0.76 | 40 | PO4 |
| 5 | 190 | 0.46 | 0.75 | 40 | empty |
Interfaces
4 interfaces between chains.
- C–D · 800 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 795 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 642 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 638 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 6B5X · PDBe 6B5X · UniProt P9WKD3
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