MolNFT v1 · #117480 · protein

Structural insights of isocitrate lyases from magnaporthe oryzae

5E9F: “Structural insights of isocitrate lyases from magnaporthe oryzae”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.88). MolNFT v1 #117480 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5E9F
Type: protein
Length: 1,957 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: MG
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Isocitrate lyase (EC 4.1.3.1, 4.1.3.30)	protein	507	50% helix, 10% strand	P0CT06
B	Isocitrate lyase (EC 4.1.3.1, 4.1.3.30)	protein	501	51% helix, 11% strand	P0CT06
C	Isocitrate lyase (EC 4.1.3.1, 4.1.3.30)	protein	496	53% helix, 11% strand	P0CT06
D	Isocitrate lyase (EC 4.1.3.1, 4.1.3.30)	protein	453	51% helix, 12% strand	P0CT06

Ligands and binding sites

MG · Magnesium ion · metal · 4 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1191	0.88	0.90	139	empty
2	722	0.88	0.91	97	empty
3	1097	0.84	0.85	122	empty
4	1183	0.84	0.85	149	MG
5	64	0.70	0.96	24	empty

Interfaces

6 interfaces between chains.

C–D · 3808 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 3750 Å² buried · 32 hydrogen bonds · protein-protein
B–C · 3102 Å² buried · 40 hydrogen bonds · protein-protein
A–D · 3014 Å² buried · 43 hydrogen bonds · protein-protein
A–C · 1476 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5E9F · 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 5E9F · PDBe 5E9F · UniProt P0CT06

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