MolNFT v1 · #63790 · protein
The crystal structure of L-threonine-O-3-phosphate decarboxylase from porphyromonas gingivalis
3FKD: “The crystal structure of L-threonine-O-3-phosphate decarboxylase from porphyromonas gingivalis”. X-ray diffraction, 18 pockets (best druggability 0.79). MolNFT v1 #63790 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3FKD
- Type
- protein
- Length
- 1,286 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-threonine-O-3-phosphate decarboxylase
- UniProt
- Q7MXY2
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-threonine-O-3-phosphate decarboxylase | protein | 326 | 41% helix, 17% strand | Q7MXY2 |
| B | L-threonine-O-3-phosphate decarboxylase | protein | 325 | 42% helix, 17% strand | Q7MXY2 |
| C | L-threonine-O-3-phosphate decarboxylase | protein | 325 | 42% helix, 18% strand | Q7MXY2 |
| D | L-threonine-O-3-phosphate decarboxylase | protein | 310 | 40% helix, 17% strand | Q7MXY2 |
Pockets
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.79 | 0.88 | 59 | empty |
| 2 | 391 | 0.79 | 0.88 | 54 | empty |
| 3 | 427 | 0.72 | 0.82 | 52 | empty |
| 4 | 330 | 0.64 | 0.80 | 47 | empty |
| 5 | 331 | 0.62 | 0.79 | 29 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1684 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1671 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 614 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 367 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 110 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 3FKD · The crystal structure of L-threonine-O-3-phosphate decarboxylase from Porphyromonas… · 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 Q7MXY2
- Elsewhere: RCSB PDB 3FKD · PDBe 3FKD · UniProt Q7MXY2
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