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Tev cleaved human ATP citrate lyase bound to tartrate and ADP

Analyse Tev cleaved human ATP citrate lyase bound to tartrate and ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

5TDZ · TEV Cleaved Human ATP Citrate Lyase Bound to Tartrate 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 5TDZ · PDBe 5TDZ · UniProt P53396

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