Research workbench
Structure of T. atroviride fdc variant tafdcv in complex with prfmn crotonic acid adduct
Analyse Structure of T. atroviride fdc variant tafdcv in complex with prfmn crotonic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NF2
- Type
- protein
- Length
- 993 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
- JRH, K, MN
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferulic acid decarboxylase 1 (EC 4.1.1.102) | protein | 497 | 33% helix, 25% strand | G9NLP8 |
| B | Ferulic acid decarboxylase 1 (EC 4.1.1.102) | protein | 496 | 31% helix, 24% strand | G9NLP8 |
Ligands and binding sites
- JRH · prFMN cofactor and crotonic acid adduct · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 6 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 | 283 | 0.85 | 0.96 | 40 | JRH, K |
| 2 | 271 | 0.84 | 0.96 | 44 | JRH, K |
| 3 | 165 | 0.64 | 0.85 | 29 | empty |
| 4 | 500 | 0.61 | 0.75 | 52 | empty |
| 5 | 142 | 0.60 | 0.84 | 38 | ACT |
Interfaces
1 interface between chains.
- A–B · 4056 Ų buried · 65 hydrogen bonds · protein-protein
Compared structures
- 7NF2 · Structure of T. atroviride Fdc variant TaFdcV in complex with prFMN crotonic 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 7NF2 · PDBe 7NF2 · UniProt G9NLP8
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