MolNFT v1 · #87046 · protein
Crystal structure of the closed form of pseudomonas aeruginosa spm-1
4BP0 · Metallo-B-lactamase: “Crystal structure of the closed form of pseudomonas aeruginosa spm-1”. X-ray diffraction, 2 ligands (ZN, CL), 9 pockets (best druggability 0.68). MolNFT v1 #87046 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4BP0
- Type
- protein
- Length
- 979 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-B-lactamase
- EC
- 3.5.2.6
- UniProt
- Q8G9Q0
- Ligands
- ZN, CL
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-B-lactamase (EC 3.5.2.6) | protein | 246 | 33% helix, 27% strand | Q8G9Q0 |
| B | Metallo-B-lactamase (EC 3.5.2.6) | protein | 245 | 33% helix, 28% strand | Q8G9Q0 |
| C, D | Metallo-B-lactamase (EC 3.5.2.6) | protein | 244 | 32% helix, 27% strand | Q8G9Q0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, C, B, D
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.68 | 0.81 | 45 | ZN, CL |
| 2 | 311 | 0.67 | 0.82 | 39 | GOL, CL |
| 3 | 478 | 0.66 | 0.78 | 53 | empty |
| 4 | 339 | 0.64 | 0.79 | 38 | GOL, CL |
| 5 | 302 | 0.61 | 0.78 | 35 | ZN, CL |
Interfaces
3 interfaces between chains.
- A–C · 406 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 404 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 243 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4BP0 · Crystal structure of the closed form of Pseudomonas aeruginosa SPM-1 · 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 Q8G9Q0
- Elsewhere: RCSB PDB 4BP0 · PDBe 4BP0 · UniProt Q8G9Q0
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