Research workbench
Crystal structure of extended-spectrum beta-lactamase bel-1 in complex with imipenem
Analyse Crystal structure of extended-spectrum beta-lactamase bel-1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EPH
- Type
- protein
- Length
- 1,034 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
- ID1, CL
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 261 | 44% helix, 20% strand | Q3SAW3 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 254 | 45% helix, 20% strand | Q3SAW3 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 257 | 44% helix, 20% strand | Q3SAW3 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 262 | 45% helix, 19% strand | Q3SAW3 |
Ligands and binding sites
- ID1 · Imipenem · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.74 | 0.79 | 77 | CL |
| 2 | 544 | 0.73 | 0.81 | 53 | empty |
| 3 | 410 | 0.58 | 0.75 | 44 | empty |
| 4 | 229 | 0.51 | 0.76 | 36 | empty |
| 5 | 97 | 0.41 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–D · 923 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 913 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 390 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 5EPH · Crystal structure of extended-spectrum beta-lactamase BEL-1 in complex with Imipenem · 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 5EPH · PDBe 5EPH · UniProt Q3SAW3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.