MolNFT v1 · #100070 · protein
Q8A hfq from pseudomonas aeruginosa
4MMK · Protein hfq: “Q8A hfq from pseudomonas aeruginosa”. X-ray diffraction, 4 ligands (ZN, K, NA), 9 pockets (best druggability 0.85). MolNFT v1 #100070 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4MMK
- Type
- protein
- Length
- 826 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein hfq
- UniProt
- Q9HUM0
- Ligands
- ZN, K, NA, SO4
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 19% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, H | Protein hfq | protein | 69 | 19% helix, 42% strand | Q9HUM0 |
| D | Protein hfq | protein | 68 | 19% helix, 43% strand | Q9HUM0 |
| F | Protein hfq | protein | 68 | 21% helix, 43% strand | Q9HUM0 |
| G | Protein hfq | protein | 66 | 20% helix, 45% strand | Q9HUM0 |
| I, K, L | Protein hfq | protein | 70 | 19% helix, 41% strand | Q9HUM0 |
| J | Protein hfq | protein | 69 | 19% helix, 45% strand | Q9HUM0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 23 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- K · Potassium ion · metal · 8 copies · chains A, B, C, D, F, L
- NA · Sodium ion · metal · 3 copies · chains G, J, K
- SO4 · Sulfate ion · ion · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.85 | 0.85 | 125 | empty |
| 2 | 1081 | 0.79 | 0.80 | 71 | empty |
| 3 | 443 | 0.68 | 0.80 | 72 | ZN, NA |
| 4 | 265 | 0.60 | 0.79 | 42 | ZN |
| 5 | 134 | 0.54 | 0.81 | 30 | ZN |
Interfaces
25 interfaces between chains.
- H–I · 898 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 891 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 881 Ų buried · 13 hydrogen bonds · protein-protein
- K–L · 879 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 859 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4MMK · Q8A Hfq from Pseudomonas aeruginosa · 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 Q9HUM0
- Elsewhere: RCSB PDB 4MMK · PDBe 4MMK · UniProt Q9HUM0
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