Research workbench
Escherichia COLI transketolase in complex with cofactor analog 2'- methoxythiamine and substrate xylulose 5-phosphate
Analyse Escherichia COLI transketolase in complex with cofactor analog 2'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TJ9
- Type
- protein
- Length
- 1,331 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transketolase 1
- EC
- 2.2.1.1
- UniProt
- P27302
- Ligands
- 5SP, NDQ, CA, NA
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transketolase 1 (EC 2.2.1.1) | protein | 664 | 47% helix, 14% strand | P27302 |
| B | Transketolase 1 (EC 2.2.1.1) | protein | 667 | 48% helix, 14% strand | P27302 |
Ligands and binding sites
- 5SP · 5-O-phosphono-D-xylulose · ligand · 2 copies · chains A, B
- NDQ · 2-[3-[(4-azanyl-2-methoxy-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 26 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.76 | 0.87 | 49 | 5SP, EDO, NDQ, CA |
| 2 | 330 | 0.75 | 0.87 | 53 | NDQ, CA, 5SP |
| 3 | 341 | 0.56 | 0.75 | 45 | EDO |
| 4 | 287 | 0.54 | 0.75 | 38 | EDO |
| 5 | 275 | 0.53 | 0.76 | 36 | EDO |
Interfaces
1 interface between chains.
- A–B · 4228 Ų buried · 77 hydrogen bonds · protein-protein
Compared structures
- 6TJ9 · Escherichia coli transketolase in complex with cofactor analog 2'-methoxythiamine and… · the same entry in another collection · chain B against B, TM-score 1.00
- P27302 · AlphaFold monomer V2.0 prediction for transketolase 1 (P27302) · 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 P27302
- Elsewhere: RCSB PDB 6TJ9 · PDBe 6TJ9 · UniProt P27302
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