MolNFT v1 · #16389 · protein

The F383A variant of type II citrate synthase complexed with NADH

1NXG: “The F383A variant of type II citrate synthase complexed with NADH”. X-ray diffraction, 2 ligands (NAI, SO4), 12 pockets (best druggability 0.78). MolNFT v1 #16389 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1NXG
Type: protein
Length: 852 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Citrate synthase
EC: 2.3.3.1
UniProt: P0ABH7
Ligands: NAI, SO4
Pockets: 12 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Citrate synthase (EC 2.3.3.1)	protein	426	45% helix, 9% strand	P0ABH7

Ligands and binding sites

NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	861	0.78	0.81	79	SO4
2	946	0.78	0.80	90	SO4
3	191	0.59	0.81	22	empty
4	152	0.53	0.80	21	empty
5	110	0.44	0.77	15	empty

Interfaces

1 interface between chains.

A–B · 6396 Å² buried · 109 hydrogen bonds · protein-protein

Compared structures

1NXG · The F383A variant of type II Citrate Synthase complexed with NADH · the same entry in another collection · chain A against A, TM-score 1.00
P0ABH7 · AlphaFold monomer V2.0 prediction for citrate synthase (P0ABH7) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P0ABH7
Elsewhere: RCSB PDB 1NXG · PDBe 1NXG · UniProt P0ABH7

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