Research workbench
2.32 ångström X-ray crystal structure of R47A mutant of human acmsd
Analyse 2.32 ångström X-ray crystal structure of R47A mutant of human acmsd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IGN
- Type
- protein
- Length
- 1,992 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
- EC
- 4.1.1.45
- UniProt
- Q8TDX5
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (EC 4.1.1.45) | protein | 332 | 47% helix, 17% strand | Q8TDX5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 809 | 0.76 | 0.80 | 51 | empty |
| 2 | 320 | 0.68 | 0.82 | 44 | empty |
| 3 | 241 | 0.68 | 0.84 | 22 | empty |
| 4 | 348 | 0.68 | 0.81 | 52 | empty |
| 5 | 385 | 0.67 | 0.80 | 48 | empty |
Interfaces
6 interfaces between chains.
- A–F · 2540 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 2538 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 2505 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 524 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 215 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4IGN · 2.32 Angstrom X-ray Crystal structure of R47A mutant of human ACMSD · the same entry in another collection · chain F against F, TM-score 1.00
- Q8TDX5 · AlphaFold monomer V2.0 prediction for 2-amino-3-carboxymuconate-6-semialdehyde… · 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 Q8TDX5
- Elsewhere: RCSB PDB 4IGN · PDBe 4IGN · UniProt Q8TDX5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.