MolNFT v1 · #61630 · protein
GDP-perosamine synthase from caulobacter crescentus with bound GDP-3- deoxyperosamine
3DR7 · Putative perosamine synthetase: “GDP-perosamine synthase from caulobacter crescentus with bound GDP-3- deoxyperosamine”. X-ray diffraction, 1 ligand (GPD), 14 pockets (best druggability 0.70). MolNFT v1 #61630 on GenesisL1: 3D…
- PDB
- 3DR7
- Type
- protein
- Length
- 1,469 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative perosamine synthetase
- UniProt
- O85354
- Ligands
- GPD
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative perosamine synthetase | protein | 368 | 42% helix, 17% strand | O85354 |
| B, C, D | Putative perosamine synthetase | protein | 367 | 42% helix, 16% strand | O85354 |
Ligands and binding sites
- GPD · (2R,3S,5S,6R)-5-amino-3-hydroxy-6-methyl-oxan-2-yl · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.70 | 0.82 | 39 | GPD |
| 2 | 382 | 0.69 | 0.82 | 45 | GPD |
| 3 | 479 | 0.68 | 0.79 | 50 | GPD |
| 4 | 344 | 0.68 | 0.82 | 38 | GPD |
| 5 | 335 | 0.62 | 0.79 | 49 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2479 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2360 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 357 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 350 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 3DR7 · GDP-perosamine synthase from Caulobacter crescentus with bound GDP-3-deoxyperosamine · 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 O85354
- Elsewhere: RCSB PDB 3DR7 · PDBe 3DR7 · UniProt O85354
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