MolNFT v1 · #160361 · protein
The evolving story of atzt, a periplasmic binding protein
6PI5 · Atrazine periplasmic binding protein: “The evolving story of atzt, a periplasmic binding protein”. X-ray diffraction, 1 ligand (GUN), 16 pockets (best druggability 0.80). MolNFT v1 #160361 on GenesisL1: 3D structure, binding sites…
- PDB
- 6PI5
- Type
- protein
- Length
- 1,333 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Atrazine periplasmic binding protein
- UniProt
- Q936X6
- Ligands
- GUN
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Atrazine periplasmic binding protein | protein | 334 | 40% helix, 23% strand | Q936X6 |
| C | Atrazine periplasmic binding protein | protein | 333 | 41% helix, 23% strand | Q936X6 |
| D | Atrazine periplasmic binding protein | protein | 332 | 41% helix, 23% strand | Q936X6 |
Ligands and binding sites
- GUN · Guanine · ligand · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.80 | 0.85 | 77 | DMS |
| 2 | 1003 | 0.76 | 0.78 | 91 | empty |
| 3 | 255 | 0.68 | 0.84 | 42 | empty |
| 4 | 174 | 0.59 | 0.82 | 35 | empty |
| 5 | 146 | 0.58 | 0.83 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–D · 559 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 470 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 446 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6PI5 · 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 6PI5 · PDBe 6PI5 · UniProt Q936X6
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