MolNFT v1 · #177218 · protein

Crystal structure of isocitrate lyase-1 from saccaromyces cervisiae

7EBC: “Crystal structure of isocitrate lyase-1 from saccaromyces cervisiae”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.91). MolNFT v1 #177218 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7EBC
Type: protein
Length: 2,101 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isocitrate lyase
EC: 4.1.3.1
UniProt: P28240
Ligands: MG
Pockets: 20 · best druggability 0.91

Structure

x-ray diffraction · 3 distinct chains · 54% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Isocitrate lyase (EC 4.1.3.1)	protein	524	55% helix, 10% strand	P28240
B, D	Isocitrate lyase (EC 4.1.3.1)	protein	527	54% helix, 10% strand	P28240
C	Isocitrate lyase (EC 4.1.3.1)	protein	523	54% helix, 10% strand	P28240

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
PG4 · Tetraethylene glycol · additive · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1156	0.91	0.94	178	empty
2	1118	0.87	0.88	151	empty
3	923	0.85	0.86	129	empty
4	148	0.77	0.95	34	empty
5	467	0.73	0.83	47	MG

Interfaces

6 interfaces between chains.

A–B · 4554 Å² buried · 54 hydrogen bonds · protein-protein
C–D · 4498 Å² buried · 45 hydrogen bonds · protein-protein
B–C · 2710 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 2704 Å² buried · 27 hydrogen bonds · protein-protein
B–D · 1637 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

7EBC · Crystal structure of Isocitrate lyase-1 from Saccaromyces cervisiae · the same entry in another collection · chain D against D, TM-score 1.00
P28240 · AlphaFold monomer V2.0 prediction for isocitrate lyase (P28240) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P28240
Elsewhere: RCSB PDB 7EBC · PDBe 7EBC · UniProt P28240

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