MolNFT v1 · #27173 · protein
Crystal structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound D-ribulose 5-phosphate
1XBV: “Crystal structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound D-ribulose 5-phosphate”. X-ray diffraction, 2 ligands (5RP, MG), 4 pockets (best druggability 0.79). MolNFT v1 #27173 on GenesisL1: 3D structure, binding…
- PDB
- 1XBV
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-keto-L-gulonate 6-phosphate decarboxylase
- UniProt
- P39304
- Ligands
- 5RP, MG
- Pockets
- 4 · best druggability 0.79
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 | protein | 213 | 50% helix, 20% strand | P39304 |
| B | 3-keto-L-gulonate 6-phosphate decarboxylase | protein | 215 | 48% helix, 20% strand | P39304 |
Ligands and binding sites
- 5RP · Ribulose-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 | 145 | 0.79 | 0.96 | 42 | 5RP, MG |
| 2 | 112 | 0.76 | 0.96 | 32 | 5RP, MG |
| 3 | 135 | 0.42 | 0.75 | 22 | empty |
| 4 | 102 | 0.41 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1510 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1XBV · Crystal structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound D-ribulose… · 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 1XBV · PDBe 1XBV · UniProt P39304
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