MolNFT v1 · #144780 · protein
Crystal structure of 3-nitropropionate modified isocitrate lyase from mycobacterium tuberculosis with pyruvate
6C4A · Isocitrate lyase 1: “Crystal structure of 3-nitropropionate modified isocitrate lyase from mycobacterium tuberculosis with pyruvate”. X-ray diffraction, 3 ligands (PYR, 3NP, MG), 20 pockets (best druggability 0.90). MolNFT v1…
- PDB
- 6C4A
- Type
- protein
- Length
- 3,423 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, 3NP, MG
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 50% 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, D, E, F, H | Isocitrate lyase 1 (EC 4.1.3.1, 4.1.3.30) | protein | 428 | 49% helix, 12% strand | H8EVV4 |
| G | Isocitrate lyase 1 (EC 4.1.3.1, 4.1.3.30) | protein | 427 | 50% helix, 12% strand | H8EVV4 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- 3NP · 3-nitropropanoic acid · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 21 copies · chains A, B, C, D, E, F, G, H
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, C, D, E, F, G, H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.90 | 0.94 | 189 | empty |
| 2 | 785 | 0.90 | 0.94 | 176 | empty |
| 3 | 387 | 0.84 | 0.93 | 77 | empty |
| 4 | 310 | 0.83 | 0.93 | 59 | empty |
| 5 | 320 | 0.82 | 0.93 | 61 | empty |
Interfaces
16 interfaces between chains.
- G–H · 5046 Ų buried · 90 hydrogen bonds · protein-protein
- E–F · 5038 Ų buried · 94 hydrogen bonds · protein-protein
- A–B · 5015 Ų buried · 96 hydrogen bonds · protein-protein
- C–D · 4999 Ų buried · 90 hydrogen bonds · protein-protein
- A–D · 2358 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
- 6C4A · 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 6C4A · PDBe 6C4A · UniProt H8EVV4
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