MolNFT v1 · #160863 · protein
Adc-7 in complex with beta-lactam antibiotic ceftazidime
6PWM · Beta-lactamase: “Adc-7 in complex with beta-lactam antibiotic ceftazidime”. X-ray diffraction, 2 ligands (CAZ, GLY), 12 pockets (best druggability 0.74). MolNFT v1 #160863 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6PWM
- Type
- protein
- Length
- 1,423 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6DRA1
- Ligands
- CAZ, GLY
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 356 | 42% helix, 20% strand | Q6DRA1 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 355 | 42% helix, 20% strand | Q6DRA1 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 42% helix, 20% strand | Q6DRA1 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 354 | 41% helix, 20% strand | Q6DRA1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.74 | 0.79 | 69 | empty |
| 2 | 642 | 0.69 | 0.78 | 78 | empty |
| 3 | 604 | 0.65 | 0.76 | 75 | CAZ |
| 4 | 426 | 0.62 | 0.77 | 61 | empty |
| 5 | 284 | 0.58 | 0.78 | 45 | CAZ, GLY |
Interfaces
5 interfaces between chains.
- C–D · 556 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 488 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 390 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 270 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 98 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6PWM · ADC-7 in complex with Beta-lactam antibiotic ceftazidime · 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 Q6DRA1
- Elsewhere: RCSB PDB 6PWM · PDBe 6PWM · UniProt Q6DRA1
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