Research workbench
Tev cleaved human ATP citrate lyase bound to 4R-hydroxycitrate and ADP
Analyse Tev cleaved human ATP citrate lyase bound to 4R-hydroxycitrate and ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TDM
- Type
- protein
- Length
- 750 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
- 7A2, ADP, ADN, MG
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-citrate synthase (EC 2.3.3.8) | protein | 427 | 37% helix, 26% strand | P53396 |
| B | ATP-citrate synthase (EC 2.3.3.8) | protein | 323 | 37% helix, 21% strand | P53396 |
Ligands and binding sites
- 7A2 · 3-C-carboxy-2-deoxy-L-threo-pentaric acid · ligand · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ADN · Adenosine · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.81 | 0.85 | 98 | ADP, MG |
| 2 | 310 | 0.71 | 0.85 | 51 | 7A2 |
| 3 | 67 | 0.54 | 0.88 | 20 | empty |
| 4 | 69 | 0.51 | 0.85 | 14 | empty |
| 5 | 98 | 0.49 | 0.82 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2274 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5TDM · TEV Cleaved Human ATP Citrate Lyase Bound to 4R-Hydroxycitrate and ADP · the same entry in another collection · chain A against A, TM-score 1.00
- P53396 · AlphaFold monomer V2.0 prediction for ATP-citrate synthase (P53396) · a predicted model of the same protein · chain B 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 P53396
- Elsewhere: RCSB PDB 5TDM · PDBe 5TDM · UniProt P53396
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