MolNFT v1 · #149817 · protein
The structure of variant R369A of the mo-insertase domain CNX1E from arabidopsis thaliana in complex with AMP
6GBF · Molybdopterin biosynthesis protein CNX1: “The structure of variant R369A of the mo-insertase domain CNX1E from arabidopsis thaliana in complex with AMP”. X-ray diffraction, 2 ligands (AMP, MG), 4 pockets (best druggability 0.53).…
- PDB
- 6GBF
- Type
- protein
- Length
- 418 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Molybdopterin biosynthesis protein CNX1
- EC
- 2.10.1.1, 2.7.7.75
- UniProt
- Q39054
- Ligands
- AMP, MG
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Molybdopterin biosynthesis protein CNX1 (EC 2.10.1.1, 2.7.7.75) | protein | 418 | 21% helix, 33% strand | Q39054 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- ACT · Acetate ion · additive · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.53 | 0.87 | 18 | empty |
| 2 | 193 | 0.51 | 0.77 | 33 | EDO |
| 3 | 71 | 0.34 | 0.77 | 20 | AMP, MG |
| 4 | 60 | 0.28 | 0.73 | 21 | ACT |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 6GBF · The Structure of variant R369A of the Mo-insertase domain Cnx1E from Arabidopsis thaliana… · the same entry in another collection · chain A against A, TM-score 1.00
- Q39054 · AlphaFold monomer V2.0 prediction for molybdopterin biosynthesis protein CNX1 (Q39054) · a predicted model of the same protein · 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 Q39054
- Elsewhere: RCSB PDB 6GBF · PDBe 6GBF · UniProt Q39054
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