MolNFT v1 · #152340 · protein
SUBSTRATE/PRODUCT bound argininosuccinate lyase from mycobacterium tuberculosis
6IEN: “SUBSTRATE/PRODUCT bound argininosuccinate lyase from mycobacterium tuberculosis”. X-ray diffraction, 3 ligands (AS1, FUM, ARG), 18 pockets (best druggability 0.76). MolNFT v1 #152340 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6IEN
- Type
- protein
- Length
- 1,740 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argininosuccinate lyase
- EC
- 4.3.2.1
- UniProt
- P9WPY7
- Ligands
- AS1, FUM, ARG
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argininosuccinate lyase (EC 4.3.2.1) | protein | 452 | 67% helix, 5% strand | P9WPY7 |
| B | Argininosuccinate lyase (EC 4.3.2.1) | protein | 454 | 69% helix, 5% strand | P9WPY7 |
| C | Argininosuccinate lyase (EC 4.3.2.1) | protein | 418 | 66% helix, 6% strand | P9WPY7 |
| D | Argininosuccinate lyase (EC 4.3.2.1) | protein | 416 | 66% helix, 6% strand | P9WPY7 |
Ligands and binding sites
- AS1 · Argininosuccinate · ligand · 3 copies · chains A, B, C, D
- FUM · Fumaric acid · ligand · chains A, C, D
- ARG · Arginine · ligand · chains A, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.76 | 0.97 | 31 | AS1 |
| 2 | 308 | 0.75 | 0.88 | 59 | FUM, ARG |
| 3 | 96 | 0.74 | 0.97 | 28 | AS1 |
| 4 | 91 | 0.74 | 0.97 | 30 | AS1 |
| 5 | 240 | 0.63 | 0.82 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4374 Ų buried · 80 hydrogen bonds · protein-protein
- C–D · 4210 Ų buried · 69 hydrogen bonds · protein-protein
- B–D · 2227 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2119 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1771 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6IEN · Substrate/product bound Argininosuccinate lyase from Mycobacterium tuberculosis · the same entry in another collection · chain A against A, TM-score 1.00
- P9WPY7 · AlphaFold monomer V2.0 prediction for argininosuccinate lyase (P9WPY7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 6IEN · PDBe 6IEN · UniProt P9WPY7
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