MolNFT v1 · #160373 · protein
The evolving story of atzt, a periplasmic binding protein
6PII · Atrazine periplasmic binding protein: “The evolving story of atzt, a periplasmic binding protein”. X-ray diffraction, 4 ligands (GUN, EMC, CA), 17 pockets (best druggability 0.61). MolNFT v1 #160373 on GenesisL1: 3D structure…
- PDB
- 6PII
- Type
- protein
- Length
- 1,332 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Atrazine periplasmic binding protein
- UniProt
- Q936X6
- Ligands
- GUN, EMC, CA, PO4
- Pockets
- 17 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Atrazine periplasmic binding protein | protein | 336 | 40% helix, 23% strand | Q936X6 |
| B | Atrazine periplasmic binding protein | protein | 334 | 40% helix, 23% strand | Q936X6 |
| C, D | Atrazine periplasmic binding protein | protein | 331 | 40% helix, 23% strand | Q936X6 |
Ligands and binding sites
- GUN · Guanine · ligand · 4 copies · chains A, B, C, D
- EMC · Ethyl mercury ion · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains C
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.61 | 0.83 | 34 | empty |
| 2 | 192 | 0.58 | 0.81 | 34 | empty |
| 3 | 129 | 0.54 | 0.82 | 27 | empty |
| 4 | 265 | 0.53 | 0.76 | 32 | empty |
| 5 | 226 | 0.50 | 0.75 | 35 | empty |
Interfaces
2 interfaces between chains.
- B–D · 654 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 640 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6PII · The evolving story of AtzT, a periplasmic binding protein · 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 Q936X6
- Elsewhere: RCSB PDB 6PII · PDBe 6PII · UniProt Q936X6
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