MolNFT v1 · #117991 · protein
Crystal structure of extended-spectrum beta-lactamase bel-1 (monoclinic form)
5EOO: “Crystal structure of extended-spectrum beta-lactamase bel-1 (monoclinic form)”. X-ray diffraction, 1 ligand (CL), 12 pockets (best druggability 0.71). MolNFT v1 #117991 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EOO
- Type
- protein
- Length
- 1,039 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q3SAW3
- Ligands
- CL
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 263 | 46% helix, 19% strand | Q3SAW3 |
| B, C | Beta-lactamase (EC 3.5.2.6) | protein | 261 | 46% helix, 19% strand | Q3SAW3 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 254 | 44% helix, 20% strand | Q3SAW3 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, D
- CIT · Citric acid · additive · 3 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, B
- IPA · Isopropyl alcohol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.71 | 0.79 | 52 | empty |
| 2 | 542 | 0.70 | 0.79 | 56 | MRD |
| 3 | 102 | 0.47 | 0.80 | 17 | PGE |
| 4 | 91 | 0.41 | 0.78 | 16 | PGE |
| 5 | 67 | 0.39 | 0.80 | 14 | empty |
Interfaces
3 interfaces between chains.
- C–D · 912 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 907 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 269 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5EOO · Crystal structure of extended-spectrum beta-lactamase BEL-1 (monoclinic form) · 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 Q3SAW3
- Elsewhere: RCSB PDB 5EOO · PDBe 5EOO · UniProt Q3SAW3
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