MolNFT v1 · #63048 · protein
Crystal structure of kgpdc from streptococcus mutans
3EXR · Rmpd (hexulose-6-phosphate synthase): “Crystal structure of kgpdc from streptococcus mutans”. X-ray diffraction, 8 pockets (best druggability 0.65). MolNFT v1 #63048 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3EXR
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rmpd (hexulose-6-phosphate synthase)
- EC
- 4.1.1.85
- UniProt
- Q93DA8
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rmpd (hexulose-6-phosphate synthase) (EC 4.1.1.85) | protein | 219 | 49% helix, 19% strand | Q93DA8 |
| B | Rmpd (hexulose-6-phosphate synthase) (EC 4.1.1.85) | protein | 212 | 47% helix, 20% strand | Q93DA8 |
| C | Rmpd (hexulose-6-phosphate synthase) (EC 4.1.1.85) | protein | 211 | 47% helix, 20% strand | Q93DA8 |
| D | Rmpd (hexulose-6-phosphate synthase) (EC 4.1.1.85) | protein | 218 | 48% helix, 19% strand | Q93DA8 |
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.65 | 0.79 | 51 | empty |
| 2 | 343 | 0.62 | 0.78 | 44 | empty |
| 3 | 282 | 0.62 | 0.80 | 36 | empty |
| 4 | 280 | 0.61 | 0.79 | 35 | empty |
| 5 | 218 | 0.56 | 0.79 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1148 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1132 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 236 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3EXR · Crystal structure of KGPDC from Streptococcus mutans · 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 Q93DA8
- Elsewhere: RCSB PDB 3EXR · PDBe 3EXR · UniProt Q93DA8
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