MolNFT v1 · #72781 · protein
Crystal structure of pseudomonas aeruginosa guanidinopropionase complexed with 1,6-diaminohexane
3NIP · 3-guanidinopropionase: “Crystal structure of pseudomonas aeruginosa guanidinopropionase complexed with 1,6-diaminohexane”. X-ray diffraction, 1 ligand (16D), 20 pockets (best druggability 0.88). MolNFT v1 #72781 on GenesisL1: 3D…
- PDB
- 3NIP
- Type
- protein
- Length
- 1,896 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-guanidinopropionase
- EC
- 3.5.3.17
- UniProt
- Q9I6K2
- Ligands
- 16D
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 3-guanidinopropionase (EC 3.5.3.17) | protein | 316 | 39% helix, 19% strand | Q9I6K2 |
Ligands and binding sites
- 16D · Hexane-1,6-diamine · ligand · 5 copies · chains B, C, E, D, F, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.88 | 0.89 | 141 | 16D |
| 2 | 499 | 0.79 | 0.86 | 44 | empty |
| 3 | 496 | 0.79 | 0.86 | 39 | empty |
| 4 | 352 | 0.77 | 0.88 | 51 | empty |
| 5 | 309 | 0.75 | 0.87 | 47 | empty |
Interfaces
12 interfaces between chains.
- D–F · 1257 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 1255 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 1244 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1230 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 1226 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3NIP · Crystal structure of Pseudomonas aeruginosa guanidinopropionase complexed with… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9I6K2 · AlphaFold monomer V2.0 prediction for guanidinopropionase (Q9I6K2) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9I6K2
- Elsewhere: RCSB PDB 3NIP · PDBe 3NIP · UniProt Q9I6K2
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