MolNFT v1 · #19009 · protein
Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L- xylulose 5-phosphate
1Q6R: “Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L- xylulose 5-phosphate”. X-ray diffraction, 2 ligands (LX1, MG), 4 pockets (best druggability 0.80). MolNFT v1 #19009 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1Q6R
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-keto-L-gulonate 6-phosphate decarboxylase
- EC
- 4.1.2.-
- UniProt
- P39304
- Ligands
- LX1, MG
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-keto-L-gulonate 6-phosphate decarboxylase (EC 4.1.2.-) | protein | 214 | 50% helix, 20% strand | P39304 |
| B | 3-keto-L-gulonate 6-phosphate decarboxylase (EC 4.1.2.-) | protein | 215 | 49% helix, 20% strand | P39304 |
Ligands and binding sites
- LX1 · L-xylulose 5-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 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 | 161 | 0.80 | 0.96 | 46 | MG, LX1 |
| 2 | 121 | 0.75 | 0.95 | 29 | MG, LX1 |
| 3 | 126 | 0.43 | 0.76 | 21 | empty |
| 4 | 136 | 0.40 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1485 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1Q6R · Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-xylulose 5-phosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P39304 · AlphaFold monomer V2.0 prediction for 3-keto-L-gulonate-6-phosphate decarboxylase ulad… · a predicted model of the same protein · chain B 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 P39304
- Elsewhere: RCSB PDB 1Q6R · PDBe 1Q6R · UniProt P39304
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