MolNFT v1 · #134719 · protein
Tev cleaved human ATP citrate lyase bound to 4S hydroxycitrate
5TDF · ATP-citrate synthase: “Tev cleaved human ATP citrate lyase bound to 4S hydroxycitrate”. X-ray diffraction, 4 ligands (7A3, ADP, ADE), 7 pockets (best druggability 0.82). MolNFT v1 #134719 on GenesisL1: 3D structure, binding sites…
- PDB
- 5TDF
- Type
- protein
- Length
- 745 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-citrate synthase
- EC
- 2.3.3.8
- UniProt
- P53396
- Ligands
- 7A3, ADP, ADE, MG
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-citrate synthase (EC 2.3.3.8) | protein | 421 | 38% helix, 26% strand | P53396 |
| B | ATP-citrate synthase (EC 2.3.3.8) | protein | 324 | 35% helix, 20% strand | P53396 |
Ligands and binding sites
- 7A3 · 3-C-carboxy-2-deoxy-D-erythro-pentaric acid · ligand · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ADE · Adenine · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.82 | 0.84 | 125 | 7A3, ADP, MG |
| 2 | 222 | 0.62 | 0.82 | 33 | empty |
| 3 | 78 | 0.54 | 0.86 | 16 | empty |
| 4 | 166 | 0.50 | 0.78 | 32 | empty |
| 5 | 93 | 0.50 | 0.82 | 20 | GOL |
Interfaces
1 interface between chains.
- A–B · 2288 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
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 P53396
- Elsewhere: RCSB PDB 5TDF · PDBe 5TDF · UniProt P53396
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