Research workbench
Crystal structure of 2-methylcitrate synthase (prpc) from pseudomonas aeruginosa in complex with oxaloacetate.
Analyse Crystal structure of 2-methylcitrate synthase (prpc) from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S87
- Type
- protein
- Length
- 1,431 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citrate synthase
- UniProt
- Q9I5E3
- Ligands
- OAA
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Citrate synthase | protein | 359 | 60% helix, 4% strand | Q9I5E3 |
| B | Citrate synthase | protein | 353 | 62% helix, 4% strand | Q9I5E3 |
| C | Citrate synthase | protein | 354 | 61% helix, 5% strand | Q9I5E3 |
| D | Citrate synthase | protein | 365 | 60% helix, 5% strand | Q9I5E3 |
Ligands and binding sites
- OAA · Oxaloacetate ion · ligand · chains C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.70 | 0.86 | 29 | GOL, OAA |
| 2 | 461 | 0.67 | 0.79 | 51 | GOL |
| 3 | 316 | 0.64 | 0.80 | 33 | GOL |
| 4 | 383 | 0.63 | 0.78 | 42 | GOL |
| 5 | 177 | 0.44 | 0.74 | 26 | GOL |
Interfaces
4 interfaces between chains.
- C–D · 3776 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 3471 Ų buried · 47 hydrogen bonds · protein-protein
- A–D · 178 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 117 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6S87 · Crystal structure of 2-methylcitrate synthase (PrpC) 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 Q9I5E3
- Elsewhere: RCSB PDB 6S87 · PDBe 6S87 · UniProt Q9I5E3
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