MolNFT v1 · #38527 · protein
Structure of acetobacter aceti citrate synthase complexed with oxaloacetate and carboxymethyldethia coenzyme a (cmx)
2H12: “Structure of acetobacter aceti citrate synthase complexed with oxaloacetate and carboxymethyldethia coenzyme…”. X-ray diffraction, 3 ligands (OAA, CMX, SO4), 20 pockets (best druggability 0.83). MolNFT v1 #38527 on GenesisL1: 3D…
- PDB
- 2H12
- Type
- protein
- Length
- 2,533 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citrate synthase
- EC
- 2.3.3.1
- UniProt
- P20901
- Ligands
- OAA, CMX, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Citrate synthase (EC 2.3.3.1) | protein | 418 | 54% helix, 11% strand | P20901 |
| B, C, E | Citrate synthase (EC 2.3.3.1) | protein | 426 | 55% helix, 10% strand | P20901 |
| D | Citrate synthase (EC 2.3.3.1) | protein | 417 | 53% helix, 11% strand | P20901 |
| F | Citrate synthase (EC 2.3.3.1) | protein | 420 | 54% helix, 10% strand | P20901 |
Ligands and binding sites
- OAA · Oxaloacetate ion · ligand · 6 copies · chains A, B, C, D, E, F
- CMX · Carboxymethyldethia coenzyme *A · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 41 copies · chains A, B, D, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 760 | 0.83 | 0.86 | 80 | empty |
| 2 | 984 | 0.75 | 0.78 | 112 | OAA, SO4, CMX |
| 3 | 761 | 0.74 | 0.79 | 67 | OAA, CMX |
| 4 | 852 | 0.74 | 0.78 | 79 | OAA, SO4, CMX |
| 5 | 680 | 0.71 | 0.78 | 58 | OAA, CMX |
Interfaces
15 interfaces between chains.
- A–B · 6161 Ų buried · 104 hydrogen bonds · protein-protein
- E–F · 6089 Ų buried · 102 hydrogen bonds · protein-protein
- C–D · 6087 Ų buried · 103 hydrogen bonds · protein-protein
- A–E · 426 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 419 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2H12 · Structure of Acetobacter aceti citrate synthase complexed with oxaloacetate and… · the same entry in another collection · chain E against E, TM-score 1.00
- P20901 · AlphaFold monomer V2.0 prediction for citrate synthase (P20901) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P20901
- Elsewhere: RCSB PDB 2H12 · PDBe 2H12 · UniProt P20901
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