Research workbench
The crystal structure of beta-lactamase from sphaerobacter thermophilus dsm 20745
Analyse The crystal structure of beta-lactamase from sphaerobacter thermophilus dsm… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EWF
- Type
- protein
- Length
- 1,059 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- UniProt
- D1C5R0
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase | protein | 268 | 40% helix, 19% strand | D1C5R0 |
| B | Beta-lactamase | protein | 263 | 40% helix, 19% strand | D1C5R0 |
| C | Beta-lactamase | protein | 265 | 40% helix, 19% strand | D1C5R0 |
| D | Beta-lactamase | protein | 263 | 43% helix, 19% strand | D1C5R0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.80 | 0.83 | 93 | SO4 |
| 2 | 485 | 0.74 | 0.83 | 47 | SO4 |
| 3 | 307 | 0.56 | 0.76 | 38 | empty |
| 4 | 119 | 0.51 | 0.81 | 28 | SO4 |
| 5 | 86 | 0.42 | 0.79 | 29 | SO4, ACY |
Interfaces
5 interfaces between chains.
- A–B · 1024 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 401 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 160 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 158 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 97 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4EWF · The crystal structure of beta-lactamase from Sphaerobacter thermophilus DSM 20745 · 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 D1C5R0
- Elsewhere: RCSB PDB 4EWF · PDBe 4EWF · UniProt D1C5R0
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