MolNFT v1 · #117481 · protein
Structural insights of isocitrate lyases from magnaporthe oryzae
5E9G: “Structural insights of isocitrate lyases from magnaporthe oryzae”. X-ray diffraction, 2 ligands (GLV, MG), 20 pockets (best druggability 0.90). MolNFT v1 #117481 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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.
| Volume (ų) | 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 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 4060 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 3061 Ų buried · 41 hydrogen bonds · protein-protein
- A–D · 3051 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 1572 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
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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