MolNFT v1 · #81393 · protein
1.5 ångström resolution crystal structure of transaldolase from francisella tularensis in covalent complex with arabinose-5-phosphate
3UPB: “1.5 ångström resolution crystal structure of transaldolase from francisella tularensis in covalent complex…”. X-ray diffraction, 1 ligand (A5P), 4 pockets (best druggability 0.86). MolNFT v1 #81393 on GenesisL1: 3D structure…
- PDB
- 3UPB
- Type
- protein
- Length
- 620 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transaldolase
- EC
- 2.2.1.2
- UniProt
- Q5NFX0
- Ligands
- A5P
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transaldolase (EC 2.2.1.2) | protein | 311 | 59% helix, 12% strand | Q5NFX0 |
| B | Transaldolase (EC 2.2.1.2) | protein | 309 | 57% helix, 12% strand | Q5NFX0 |
Ligands and binding sites
- A5P · Arabinose-5-phosphate · ligand · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- P6G · Hexaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.86 | 0.99 | 26 | empty |
| 2 | 131 | 0.46 | 0.77 | 27 | A5P |
| 3 | 119 | 0.46 | 0.78 | 25 | A5P |
| 4 | 99 | 0.35 | 0.74 | 15 | PGE |
Interfaces
1 interface between chains.
- A–B · 852 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3UPB · 1.5 Angstrom Resolution Crystal Structure of Transaldolase from Francisella tularensis in… · 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 Q5NFX0
- Elsewhere: RCSB PDB 3UPB · PDBe 3UPB · UniProt Q5NFX0
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