MolNFT v1 · #80334 · protein
Crystal structure of spud in complex with putrescine
3TTM · Polyamine transport protein: “Crystal structure of spud in complex with putrescine”. X-ray diffraction, 1 ligand (PUT), 3 pockets (best druggability 0.81). MolNFT v1 #80334 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3TTM
- Type
- protein
- Length
- 682 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyamine transport protein
- UniProt
- Q9I6J1
- Ligands
- PUT
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Polyamine transport protein | protein | 341 | 47% helix, 18% strand | Q9I6J1 |
Ligands and binding sites
- PUT · 1,4-diaminobutane · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.81 | 0.84 | 82 | empty |
| 2 | 184 | 0.48 | 0.76 | 33 | empty |
| 3 | 76 | 0.37 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 457 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3TTM · Crystal structure of SpuD in complex with putrescine · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I6J1 · AlphaFold monomer V2.0 prediction for putrescine-binding periplasmic protein spud (Q9I6J1) · a predicted model of the same protein · 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 Q9I6J1
- Elsewhere: RCSB PDB 3TTM · PDBe 3TTM · UniProt Q9I6J1
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