Research workbench
Acmsd in complex with diflunisal derivative 14
Analyse Acmsd in complex with diflunisal derivative 14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K13
- Type
- protein
- Length
- 992 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
- EC
- 4.-.-.-
- UniProt
- Q83V25
- Ligands
- VR7, ZN
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase (EC 4.-.-.-) | protein | 330 | 45% helix, 16% strand | Q83V25 |
| B, C | 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase (EC 4.-.-.-) | protein | 331 | 46% helix, 16% strand | Q83V25 |
Ligands and binding sites
- VR7 · 2-hydroxy-5-(thiophen-3-yl)benzoic acid · ligand · chains B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.70 | 0.79 | 57 | VR7 |
| 2 | 357 | 0.65 | 0.80 | 38 | empty |
| 3 | 406 | 0.65 | 0.79 | 50 | empty |
| 4 | 429 | 0.65 | 0.78 | 48 | empty |
| 5 | 146 | 0.46 | 0.77 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2551 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 384 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7K13 · ACMSD in complex with diflunisal derivative 14 · the same entry in another collection · chain B against B, 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 Q83V25
- Elsewhere: RCSB PDB 7K13 · PDBe 7K13 · UniProt Q83V25
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