Research workbench
Fic protein from shewanella oneidensis (E73G mutant) in complex with amppnp
Analyse Fic protein from shewanella oneidensis (E73G mutant) in complex with amppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZEC
- Type
- protein
- Length
- 740 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine monophosphate-protein transferase sofic
- EC
- 2.7.7.-
- UniProt
- Q8E9K5
- Ligands
- ANP, MG
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine monophosphate-protein transferase sofic (EC 2.7.7.-) | protein | 369 | 62% helix, 4% strand | Q8E9K5 |
| B | Adenosine monophosphate-protein transferase sofic (EC 2.7.7.-) | protein | 371 | 61% helix, 5% strand | Q8E9K5 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.66 | 0.82 | 28 | ANP, MG |
| 2 | 292 | 0.64 | 0.81 | 27 | ANP |
| 3 | 312 | 0.58 | 0.77 | 32 | empty |
| 4 | 155 | 0.48 | 0.77 | 25 | empty |
| 5 | 128 | 0.41 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 913 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3ZEC · Fic protein from SHEWANELLA ONEIDENSIS (E73G mutant) in complex with AMPPNP · the same entry in another collection · chain A against A, TM-score 1.00
- Q8E9K5 · AlphaFold monomer V2.0 prediction for protein adenylyltransferase sofic (Q8E9K5) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8E9K5
- Elsewhere: RCSB PDB 3ZEC · PDBe 3ZEC · UniProt Q8E9K5
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