Research workbench
Crystal structure of type II citrate synthase (hycs) from hymenobacter sp. pamc 26554
Analyse Crystal structure of type II citrate synthase (hycs) from hymenobacter sp. pamc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E8N
- Type
- protein
- Length
- 1,280 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citrate synthase
- UniProt
- A0A142HAE2
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Citrate synthase | protein | 428 | 56% helix, 11% strand | A0A142HAE2 |
| B | Citrate synthase | protein | 424 | 54% helix, 7% strand | A0A142HAE2 |
| C | Citrate synthase | protein | 428 | 53% helix, 11% strand | A0A142HAE2 |
Ligands and binding sites
- CIT · Citric acid · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.73 | 0.97 | 22 | empty |
| 2 | 1149 | 0.72 | 0.76 | 81 | CIT |
| 3 | 367 | 0.67 | 0.81 | 61 | CIT |
| 4 | 325 | 0.65 | 0.80 | 39 | CIT |
| 5 | 263 | 0.58 | 0.79 | 48 | empty |
Interfaces
2 interfaces between chains.
- A–C · 6189 Ų buried · 95 hydrogen bonds · protein-protein
- B–C · 537 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 7E8N · Crystal structure of Type II citrate synthase (HyCS) from Hymenobacter sp. PAMC 26554 · 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 A0A142HAE2
- Elsewhere: RCSB PDB 7E8N · PDBe 7E8N · UniProt A0A142HAE2
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