Research workbench
Crystal structure of 3-nitropropionate modified isocitrate lyase from mycobacterium tuberculosis with glyoxylate and pyruvate
Analyse Crystal structure of 3-nitropropionate modified isocitrate lyase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C4C
- Type
- protein
- Length
- 3,421 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate lyase 1
- EC
- 4.1.3.1, 4.1.3.30
- UniProt
- H8EVV4
- Ligands
- PYR, GLV, 3NP, MG
- Pockets
- 20 · best druggability 0.92
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate lyase 1 (EC 4.1.3.1, 4.1.3.30) | protein | 428 | 50% helix, 12% strand | H8EVV4 |
| B, C, G | Isocitrate lyase 1 (EC 4.1.3.1, 4.1.3.30) | protein | 427 | 49% helix, 12% strand | H8EVV4 |
| D, E, F, H | Isocitrate lyase 1 (EC 4.1.3.1, 4.1.3.30) | protein | 428 | 50% helix, 12% strand | H8EVV4 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 5 copies · chains B, C, E, F, G
- GLV · Glyoxylic acid · ligand · 3 copies · chains A, D, H
- 3NP · 3-nitropropanoic acid · ligand · chains E, F
- MG · Magnesium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.92 | 0.94 | 227 | empty |
| 2 | 959 | 0.90 | 0.92 | 160 | empty |
| 3 | 909 | 0.89 | 0.92 | 150 | empty |
| 4 | 299 | 0.82 | 0.93 | 61 | empty |
| 5 | 312 | 0.81 | 0.92 | 31 | empty |
Interfaces
16 interfaces between chains.
- C–D · 5061 Ų buried · 88 hydrogen bonds · protein-protein
- G–H · 5061 Ų buried · 86 hydrogen bonds · protein-protein
- E–F · 5035 Ų buried · 91 hydrogen bonds · protein-protein
- A–B · 5009 Ų buried · 89 hydrogen bonds · protein-protein
- B–C · 2320 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
- 6C4C · Crystal structure of 3-nitropropionate modified isocitrate lyase from Mycobacterium… · the same entry in another collection · chain H against H, TM-score 1.00
- H8EVV4 · AlphaFold monomer V2.0 prediction for isocitrate lyase 1 (H8EVV4) · a predicted model of the same protein · chain G 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 H8EVV4
- Elsewhere: RCSB PDB 6C4C · PDBe 6C4C · UniProt H8EVV4
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