MolNFT v1 · #142675 · protein
Crystal structure of citrate synthase (MSED_1522) from metallosphaera sedula in complex with oxaloacetate
6ABY: “Crystal structure of citrate synthase (MSED_1522) from metallosphaera sedula in complex with oxaloacetate”. X-ray diffraction, 2 ligands (OAA, ACO), 5 pockets (best druggability 0.66). MolNFT v1 #142675 on GenesisL1: 3D structure…
- PDB
- 6ABY
- Type
- protein
- Length
- 743 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citrate synthase
- EC
- 2.3.3.16
- UniProt
- A4YGX6
- Ligands
- OAA, ACO
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Citrate synthase (EC 2.3.3.16) | protein | 371 | 59% helix, 6% strand | A4YGX6 |
| A | Citrate synthase (EC 2.3.3.16) | protein | 372 | 59% helix, 6% strand | A4YGX6 |
Ligands and binding sites
- OAA · Oxaloacetate ion · ligand · 2 copies · chains B, A
- ACO · Acetyl coenzyme *A · ligand · 2 copies · chains B, A
- GOL · Glycerol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.66 | 0.82 | 44 | OAA, ACO |
| 2 | 226 | 0.60 | 0.81 | 28 | OAA |
| 3 | 218 | 0.50 | 0.76 | 32 | GOL |
| 4 | 221 | 0.50 | 0.76 | 34 | empty |
| 5 | 98 | 0.36 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 4703 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 6ABY · Crystal structure of citrate synthase (Msed_1522) from Metallosphaera sedula in complex… · the same entry in another collection · chain B against B, 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 A4YGX6
- Elsewhere: RCSB PDB 6ABY · PDBe 6ABY · UniProt A4YGX6
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