Research workbench
Crystal structure of candida glabrata FMN adenylyltransferase in complex with FMN and ATP analog ampcpp
Analyse Crystal structure of candida glabrata FMN adenylyltransferase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G5A
- Type
- protein
- Length
- 1,776 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FMN adenylyltransferase
- EC
- 2.7.7.2
- UniProt
- Q6FNA9
- Ligands
- APC, FMN, MG, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FMN adenylyltransferase (EC 2.7.7.2) | protein | 296 | 39% helix, 9% strand | Q6FNA9 |
| B | FMN adenylyltransferase (EC 2.7.7.2) | protein | 305 | 39% helix, 10% strand | Q6FNA9 |
| C | FMN adenylyltransferase (EC 2.7.7.2) | protein | 291 | 39% helix, 9% strand | Q6FNA9 |
| D | FMN adenylyltransferase (EC 2.7.7.2) | protein | 301 | 40% helix, 9% strand | Q6FNA9 |
| E | FMN adenylyltransferase (EC 2.7.7.2) | protein | 286 | 40% helix, 9% strand | Q6FNA9 |
| F | FMN adenylyltransferase (EC 2.7.7.2) | protein | 297 | 39% helix, 9% strand | Q6FNA9 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 6 copies · chains A, B, C, D, E, F
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.86 | 0.87 | 101 | empty |
| 2 | 882 | 0.86 | 0.88 | 87 | empty |
| 3 | 359 | 0.80 | 0.90 | 64 | empty |
| 4 | 956 | 0.79 | 0.81 | 71 | APC, FMN, MG |
| 5 | 336 | 0.76 | 0.87 | 42 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1169 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1120 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 975 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 808 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 788 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3G5A · Crystal Structure of Candida glabrata FMN Adenylyltransferase in complex with FMN and ATP… · 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 Q6FNA9
- Elsewhere: RCSB PDB 3G5A · PDBe 3G5A · UniProt Q6FNA9
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