Research workbench
Eukaryotic fic domain containing protein with bound apcpp
Analyse Eukaryotic fic domain containing protein with bound apcpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U0Z
- Type
- protein
- Length
- 2,591 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosine monophosphate-protein transferase ficd
- EC
- 2.7.7.-
- UniProt
- Q9BVA6
- Ligands
- APC, MG
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 8 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosine monophosphate-protein transferase ficd (EC 2.7.7.-) | protein | 322 | 71% helix, 1% strand | Q9BVA6 |
| B | Adenosine monophosphate-protein transferase ficd (EC 2.7.7.-) | protein | 326 | 69% helix, 1% strand | Q9BVA6 |
| C | Adenosine monophosphate-protein transferase ficd (EC 2.7.7.-) | protein | 329 | 69% helix, 1% strand | Q9BVA6 |
| D | Adenosine monophosphate-protein transferase ficd (EC 2.7.7.-) | protein | 325 | 70% helix, 1% strand | Q9BVA6 |
| E | Adenosine monophosphate-protein transferase ficd (EC 2.7.7.-) | protein | 327 | 70% helix, 1% strand | Q9BVA6 |
| F | Adenosine monophosphate-protein transferase ficd (EC 2.7.7.-) | protein | 322 | 70% helix, 1% strand | Q9BVA6 |
| G | Adenosine monophosphate-protein transferase ficd (EC 2.7.7.-) | protein | 322 | 70% helix, 1% strand | Q9BVA6 |
| H | Adenosine monophosphate-protein transferase ficd (EC 2.7.7.-) | protein | 318 | 72% helix, 1% strand | Q9BVA6 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.68 | 0.80 | 47 | empty |
| 2 | 142 | 0.60 | 0.84 | 25 | empty |
| 3 | 287 | 0.60 | 0.79 | 39 | APC, MG |
| 4 | 164 | 0.60 | 0.83 | 27 | empty |
| 5 | 198 | 0.60 | 0.82 | 27 | APC, MG |
Interfaces
11 interfaces between chains.
- B–H · 868 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 446 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 443 Ų buried · 6 hydrogen bonds · protein-protein
- E–G · 437 Ų buried · 5 hydrogen bonds · protein-protein
- D–G · 409 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4U0Z · Eukaryotic Fic Domain containing protein with bound APCPP · the same entry in another collection · chain H against H, TM-score 1.00
- Q9BVA6 · AlphaFold monomer V2.0 prediction for protein adenylyltransferase ficd (Q9BVA6) · a predicted model of the same protein · chain H against A, TM-score 0.98
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 4U0Z · PDBe 4U0Z · UniProt Q9BVA6
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