MolNFT v1 · #158025 · protein
Crystal structure of the beta lactamase class D ybxi from agrobacterium fabrum
6NHU · Beta-lactamase: “Crystal structure of the beta lactamase class D ybxi from agrobacterium fabrum”. X-ray diffraction, 1 ligand (PO4), 6 pockets (best druggability 0.71). MolNFT v1 #158025 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6NHU
- Type
- protein
- Length
- 974 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q7D0B8
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 243 | 35% helix, 26% strand | Q7D0B8 |
| C, D | Beta-lactamase (EC 3.5.2.6) | protein | 244 | 35% helix, 26% strand | Q7D0B8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains B, D, A, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains B, D, C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.71 | 0.85 | 36 | PO4, EDO |
| 2 | 273 | 0.71 | 0.85 | 34 | GOL, PO4 |
| 3 | 237 | 0.50 | 0.75 | 34 | empty |
| 4 | 174 | 0.43 | 0.74 | 35 | empty |
| 5 | 125 | 0.43 | 0.76 | 18 | empty |
Interfaces
4 interfaces between chains.
- B–D · 905 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 865 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 352 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 294 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6NHU · Crystal Structure of the Beta Lactamase Class D YbxI from Agrobacterium fabrum · 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 Q7D0B8
- Elsewhere: RCSB PDB 6NHU · PDBe 6NHU · UniProt Q7D0B8
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