MolNFT v1 · #163539 · protein
Crystal structure of 2-methylcitrate dehydratase (prpd) from pseudomonas aeruginosa in apo form.
6S62 · Propionate catabolic protein prpd: “Crystal structure of 2-methylcitrate dehydratase (prpd) from pseudomonas aeruginosa in apo form.”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #163539 on GenesisL1: 3D…
- PDB
- 6S62
- Type
- protein
- Length
- 2,906 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Propionate catabolic protein prpd
- UniProt
- Q9I5E6
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Propionate catabolic protein prpd | protein | 485 | 55% helix, 8% strand | Q9I5E6 |
| B | Propionate catabolic protein prpd | protein | 484 | 55% helix, 9% strand | Q9I5E6 |
| C | Propionate catabolic protein prpd | protein | 483 | 56% helix, 9% strand | Q9I5E6 |
| D | Propionate catabolic protein prpd | protein | 484 | 55% helix, 9% strand | Q9I5E6 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.85 | 0.94 | 54 | empty |
| 2 | 335 | 0.85 | 0.94 | 54 | empty |
| 3 | 286 | 0.84 | 0.95 | 41 | empty |
| 4 | 516 | 0.83 | 0.90 | 67 | empty |
| 5 | 148 | 0.78 | 0.95 | 26 | empty |
Interfaces
12 interfaces between chains.
- E–F · 3013 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2964 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2950 Ų buried · 45 hydrogen bonds · protein-protein
- A–E · 757 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 724 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6S62 · Crystal structure of 2-methylcitrate dehydratase (PrpD) from Pseudomonas aeruginosa in… · 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 Q9I5E6
- Elsewhere: RCSB PDB 6S62 · PDBe 6S62 · UniProt Q9I5E6
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