MolNFT v1 · #152339 · protein
Argininosuccinate lyase from mycobacterium tuberculosis
6IEM: “Argininosuccinate lyase from mycobacterium tuberculosis”. X-ray diffraction, 1 ligand (P3G), 20 pockets (best druggability 0.82). MolNFT v1 #152339 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IEM
- Type
- protein
- Length
- 3,617 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argininosuccinate lyase
- EC
- 4.3.2.1
- UniProt
- P9WPY7
- Ligands
- P3G
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 69% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | Argininosuccinate lyase (EC 4.3.2.1) | protein | 450 | 70% helix, 5% strand | P9WPY7 |
| B | Argininosuccinate lyase (EC 4.3.2.1) | protein | 462 | 68% helix, 6% strand | P9WPY7 |
| D, H | Argininosuccinate lyase (EC 4.3.2.1) | protein | 454 | 70% helix, 6% strand | P9WPY7 |
| E | Argininosuccinate lyase (EC 4.3.2.1) | protein | 448 | 69% helix, 5% strand | P9WPY7 |
| G | Argininosuccinate lyase (EC 4.3.2.1) | protein | 449 | 69% helix, 5% strand | P9WPY7 |
Ligands and binding sites
- P3G · 3,6,9,12,15-pentaoxaheptadecane · ligand · chains D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, D, C, E, F
- GOL · Glycerol · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, C, F
- 2PE · Nonaethylene glycol · additive · chains E
- PGE · Triethylene glycol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.82 | 0.84 | 86 | empty |
| 2 | 899 | 0.76 | 0.79 | 85 | empty |
| 3 | 881 | 0.75 | 0.79 | 92 | GOL |
| 4 | 889 | 0.74 | 0.78 | 92 | empty |
| 5 | 885 | 0.74 | 0.78 | 96 | empty |
Interfaces
14 interfaces between chains.
- A–B · 4026 Ų buried · 69 hydrogen bonds · protein-protein
- C–D · 3919 Ų buried · 71 hydrogen bonds · protein-protein
- G–H · 3910 Ų buried · 75 hydrogen bonds · protein-protein
- E–F · 3904 Ų buried · 75 hydrogen bonds · protein-protein
- B–D · 1951 Ų buried · 34 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 P9WPY7
- Elsewhere: RCSB PDB 6IEM · PDBe 6IEM · UniProt P9WPY7
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