Research workbench
Structure of T. atroviride variant tafdcv in complex with prfmn- butynoic acid adduct
Analyse Structure of T. atroviride variant tafdcv in complex with prfmn- butynoic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NF1
- Type
- protein
- Length
- 994 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferulic acid decarboxylase 1
- EC
- 4.1.1.102
- UniProt
- G9NLP8
- Ligands
- JRK, K, MN
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ferulic acid decarboxylase 1 (EC 4.1.1.102) | protein | 497 | 33% helix, 24% strand | G9NLP8 |
Ligands and binding sites
- JRK · prFMN cofactor and butynoic acid adduct · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 7 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.86 | 0.96 | 38 | JRK, K |
| 2 | 316 | 0.85 | 0.95 | 44 | JRK, K |
| 3 | 142 | 0.61 | 0.85 | 29 | empty |
| 4 | 144 | 0.59 | 0.84 | 31 | empty |
| 5 | 283 | 0.52 | 0.75 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 4206 Ų buried · 63 hydrogen bonds · protein-protein
Compared structures
- 7NF1 · Structure of T. atroviride variant TaFdcV in complex with prFMN-butynoic acid adduct · the same entry in another collection · chain A 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 G9NLP8
- Elsewhere: RCSB PDB 7NF1 · PDBe 7NF1 · UniProt G9NLP8
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