MolNFT v1 · #166853 · protein
X-ray structure of a sugar N-formyltransferase from shewanella sp FDAARGOS_354
6V2T · Dtdp-4-amino-4,6-dideoxyglucose formyltransferase: “X-ray structure of a sugar N-formyltransferase from shewanella sp FDAARGOS_354”. X-ray diffraction, 4 ligands (0FX, FOL, NA), 4 pockets (best druggability 0.71). MolNFT v1 #166853…
- PDB
- 6V2T
- Type
- protein
- Length
- 497 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-4-amino-4,6-dideoxyglucose formyltransferase
- UniProt
- A0A1Z4A6S6
- Ligands
- 0FX, FOL, NA, PO4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dtdp-4-amino-4,6-dideoxyglucose formyltransferase | protein | 246 | 33% helix, 27% strand | A0A1Z4A6S6 |
| B | Dtdp-4-amino-4,6-dideoxyglucose formyltransferase | protein | 251 | 32% helix, 26% strand | A0A1Z4A6S6 |
Ligands and binding sites
- 0FX · dTDP-4-amino-4,6-dideoxyglucose · ligand · 2 copies · chains A, B
- FOL · Folic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- PO4 · Phosphate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.71 | 0.81 | 45 | 0FX, FOL |
| 2 | 393 | 0.71 | 0.82 | 40 | 0FX, FOL |
| 3 | 50 | 0.39 | 0.82 | 15 | empty |
| 4 | 84 | 0.31 | 0.73 | 20 | PO4 |
Interfaces
1 interface between chains.
- A–B · 1480 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6V2T · X-ray structure of a sugar N-formyltransferase from Shewanella sp FDAARGOS_354 · 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 A0A1Z4A6S6
- Elsewhere: RCSB PDB 6V2T · PDBe 6V2T · UniProt A0A1Z4A6S6
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