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Structure of a beta-lactamase class a-like protein from veillonella parvula.
Analyse Structure of a beta-lactamase class a-like protein from veillonella parvula. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HES
- Type
- protein
- Length
- 1,354 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase class a-like protein
- UniProt
- D1BLB4
- Ligands
- NA
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase class a-like protein | protein | 275 | 47% helix, 19% strand | D1BLB4 |
| C, D, E | Beta-lactamase class a-like protein | protein | 268 | 46% helix, 20% strand | D1BLB4 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 17 copies · chains A, B, C, D, E
- FMT · Formic acid · additive · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.80 | 0.82 | 102 | GOL, NA, FMT |
| 2 | 1091 | 0.76 | 0.79 | 104 | GOL |
| 3 | 915 | 0.74 | 0.78 | 71 | GOL |
| 4 | 79 | 0.51 | 0.84 | 17 | FMT, NA |
| 5 | 234 | 0.45 | 0.73 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1213 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1197 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 435 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 374 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 368 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 62 modified (engineered).
Compared structures
- 4HES · Structure of a Beta-Lactamase Class A-like Protein from Veillonella parvula. · 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 D1BLB4
- Elsewhere: RCSB PDB 4HES · PDBe 4HES · UniProt D1BLB4
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