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Structural insights of isocitrate lyases from magnaporthe oryzae

Analyse Structural insights of isocitrate lyases from magnaporthe oryzae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5E9G
Type: protein
Length: 2,034 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isocitrate lyase
EC: 4.1.3.1, 4.1.3.30
UniProt: P0CT06
Ligands: GLV, MG
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Isocitrate lyase (EC 4.1.3.1, 4.1.3.30)	protein	524	52% helix, 10% strand	P0CT06
B	Isocitrate lyase (EC 4.1.3.1, 4.1.3.30)	protein	525	53% helix, 10% strand	P0CT06
C	Isocitrate lyase (EC 4.1.3.1, 4.1.3.30)	protein	499	52% helix, 10% strand	P0CT06
D	Isocitrate lyase (EC 4.1.3.1, 4.1.3.30)	protein	486	50% helix, 10% strand	P0CT06

Ligands and binding sites

GLV · Glyoxylic acid · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 3 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	970	0.90	0.92	137	empty
2	550	0.87	0.92	91	empty
3	959	0.86	0.87	122	empty
4	907	0.86	0.87	112	empty
5	93	0.74	0.96	26	GLV, MG

Interfaces

6 interfaces between chains.

A–B · 4150 Å² buried · 37 hydrogen bonds · protein-protein
C–D · 4060 Å² buried · 42 hydrogen bonds · protein-protein
B–C · 3061 Å² buried · 41 hydrogen bonds · protein-protein
A–D · 3051 Å² buried · 45 hydrogen bonds · protein-protein
A–C · 1572 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5E9G · Structural insights of isocitrate lyases from Magnaporthe oryzae · the same entry in another collection · chain D against D, TM-score 1.00
P0CT06 · AlphaFold monomer V2.0 prediction for isocitrate lyase (P0CT06) · a predicted model of the same protein · chain A 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 P0CT06
Elsewhere: RCSB PDB 5E9G · PDBe 5E9G · UniProt P0CT06

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