MolNFT v1 · #116339 · protein
Crystal structure of nald, the secondary repressor of mexab-oprm multidrug efflux pump in pseudomonas aeruginosa
5DAJ: “Crystal structure of nald, the secondary repressor of mexab-oprm multidrug efflux pump in pseudomonas…”. X-ray diffraction, 12 pockets (best druggability 0.87). MolNFT v1 #116339 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5DAJ
- Type
- protein
- Length
- 1,559 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nald
- UniProt
- Q9HY46
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nald | protein | 197 | 77% helix, 1% strand | Q9HY46 |
| B | Nald | protein | 195 | 77% helix, 1% strand | Q9HY46 |
| C | Nald | protein | 195 | 77% helix, 1% strand | Q9HY46 |
| D | Nald | protein | 192 | 77% helix, 1% strand | Q9HY46 |
| E | Nald | protein | 193 | 77% helix, 1% strand | Q9HY46 |
| F | Nald | protein | 193 | 77% helix, 1% strand | Q9HY46 |
| G | Nald | protein | 198 | 75% helix, 1% strand | Q9HY46 |
| H | Nald | protein | 196 | 77% helix, 1% strand | Q9HY46 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 729 | 0.87 | 0.91 | 73 | empty |
| 2 | 779 | 0.87 | 0.90 | 77 | empty |
| 3 | 641 | 0.86 | 0.91 | 64 | empty |
| 4 | 771 | 0.86 | 0.88 | 75 | empty |
| 5 | 917 | 0.75 | 0.78 | 77 | empty |
Interfaces
10 interfaces between chains.
- G–H · 2044 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2016 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2015 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 1983 Ų buried · 26 hydrogen bonds · protein-protein
- A–H · 539 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
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 Q9HY46
- Elsewhere: RCSB PDB 5DAJ · PDBe 5DAJ · UniProt Q9HY46
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