MolNFT v1 · #134739 · protein
Tev cleaved human ATP citrate lyase bound to tartrate and ADP
5TDZ · ATP-citrate synthase: “Tev cleaved human ATP citrate lyase bound to tartrate and ADP”. X-ray diffraction, 4 ligands (ADP, ADN, MG), 7 pockets (best druggability 0.80). MolNFT v1 #134739 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5TDZ
- Type
- protein
- Length
- 742 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
- ADP, ADN, MG, PO4
- Pockets
- 7 · best druggability 0.80
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 | 418 | 38% helix, 26% strand | P53396 |
| B | ATP-citrate synthase (EC 2.3.3.8) | protein | 324 | 36% helix, 20% strand | P53396 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ADN · Adenosine · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.80 | 0.83 | 93 | ADP, MG |
| 2 | 329 | 0.72 | 0.85 | 54 | TLA, PO4 |
| 3 | 138 | 0.56 | 0.82 | 26 | empty |
| 4 | 85 | 0.55 | 0.86 | 16 | PGE |
| 5 | 279 | 0.55 | 0.76 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 2270 Ų buried · 30 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 5TDZ · PDBe 5TDZ · UniProt P53396
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