MolNFT v1 · #107135 · protein
Crystal structure of adc-7 beta-lactamase
4U0T: “Crystal structure of adc-7 beta-lactamase”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.74). MolNFT v1 #107135 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4U0T
- Type
- protein
- Length
- 2,819 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adc-7 beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6DRA1
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 8 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adc-7 beta-lactamase (EC 3.5.2.6) | protein | 357 | 42% helix, 20% strand | Q6DRA1 |
| B | Adc-7 beta-lactamase (EC 3.5.2.6) | protein | 358 | 42% helix, 21% strand | Q6DRA1 |
| C | Adc-7 beta-lactamase (EC 3.5.2.6) | protein | 352 | 42% helix, 21% strand | Q6DRA1 |
| D | Adc-7 beta-lactamase (EC 3.5.2.6) | protein | 346 | 41% helix, 20% strand | Q6DRA1 |
| E | Adc-7 beta-lactamase (EC 3.5.2.6) | protein | 354 | 42% helix, 20% strand | Q6DRA1 |
| F | Adc-7 beta-lactamase (EC 3.5.2.6) | protein | 355 | 43% helix, 20% strand | Q6DRA1 |
| G | Adc-7 beta-lactamase (EC 3.5.2.6) | protein | 348 | 42% helix, 21% strand | Q6DRA1 |
| H | Adc-7 beta-lactamase (EC 3.5.2.6) | protein | 349 | 43% helix, 20% strand | Q6DRA1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.74 | 0.80 | 91 | empty |
| 2 | 525 | 0.73 | 0.81 | 50 | empty |
| 3 | 1166 | 0.70 | 0.75 | 117 | empty |
| 4 | 405 | 0.66 | 0.80 | 54 | empty |
| 5 | 391 | 0.63 | 0.78 | 48 | empty |
Interfaces
17 interfaces between chains.
- A–C · 488 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 485 Ų buried · 7 hydrogen bonds · protein-protein
- D–G · 480 Ų buried · 4 hydrogen bonds · protein-protein
- C–H · 446 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 443 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4U0T · Crystal structure of ADC-7 beta-lactamase · the same entry in another collection · chain B against B, 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 Q6DRA1
- Elsewhere: RCSB PDB 4U0T · PDBe 4U0T · UniProt Q6DRA1
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