Research workbench
Crystal structure of dimeric ficd mutant K256A complexed with mgatp
Analyse Crystal structure of dimeric ficd mutant K256A complexed with mgatp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I7I
- Type
- protein
- Length
- 334 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine monophosphate-protein transferase ficd
- EC
- 2.7.7.-, 3.1.4.-
- UniProt
- Q9BVA6
- Ligands
- ATP, MG
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine monophosphate-protein transferase ficd (EC 2.7.7.-, 3.1.4.-) | protein | 334 | 71% helix, 1% strand | Q9BVA6 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.68 | 0.86 | 29 | empty |
| 2 | 228 | 0.63 | 0.82 | 27 | MG, ATP |
| 3 | 252 | 0.50 | 0.74 | 21 | empty |
| 4 | 66 | 0.48 | 0.84 | 20 | empty |
| 5 | 124 | 0.40 | 0.74 | 16 | empty |
Compared structures
- 6I7I · Crystal structure of dimeric FICD mutant K256A complexed with MgATP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BVA6 · AlphaFold monomer V2.0 prediction for protein adenylyltransferase ficd (Q9BVA6) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9BVA6
- Elsewhere: RCSB PDB 6I7I · PDBe 6I7I · UniProt Q9BVA6
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