MolNFT v1 · #76718 · protein
Crystal structure of putative modulator of gyrase (pmba) from pseudomonas aeruginosa PAO1
3QTD · Pmba protein: “Crystal structure of putative modulator of gyrase (pmba) from pseudomonas aeruginosa PAO1”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #76718 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3QTD
- Type
- protein
- Length
- 1,766 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pmba protein
- UniProt
- Q9HVU9
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pmba protein | protein | 442 | 26% helix, 39% strand | Q9HVU9 |
| B, D | Pmba protein | protein | 441 | 26% helix, 39% strand | Q9HVU9 |
Ligands and binding sites
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.84 | 0.85 | 128 | GOL |
| 2 | 522 | 0.79 | 0.86 | 67 | empty |
| 3 | 444 | 0.78 | 0.86 | 49 | empty |
| 4 | 615 | 0.67 | 0.77 | 82 | GOL |
| 5 | 464 | 0.64 | 0.77 | 58 | GOL |
Interfaces
5 interfaces between chains.
- B–C · 1667 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 587 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 517 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 351 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 36 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 3QTD · Crystal structure of putative modulator of gyrase (PmbA) from Pseudomonas aeruginosa PAO1 · 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 Q9HVU9
- Elsewhere: RCSB PDB 3QTD · PDBe 3QTD · UniProt Q9HVU9
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