Research workbench
Deampylation complex of monomeric ficd and ampylated bip (state 2)
Analyse Deampylation complex of monomeric ficd and ampylated bip (state 2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B80
- Type
- protein
- Length
- 863 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmic reticulum chaperone bip; Protein adenylyltransferase ficd
- EC
- 3.6.4.10, 2.7.7.-, 3.1.4.-
- UniProt
- G3I8R9, Q9BVA6
- Ligands
- AMP, K, MG, PO4
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Endoplasmic reticulum chaperone bip (EC 3.6.4.10) | protein | 523 | 33% helix, 32% strand | G3I8R9 |
| A | Protein adenylyltransferase ficd (EC 2.7.7.-, 3.1.4.-) | protein | 340 | 70% helix, 1% strand | Q9BVA6 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains B, A
- K · Potassium ion · metal · 3 copies · chains B
- MG · Magnesium ion · metal · 2 copies · chains B, A
- PO4 · Phosphate ion · ion · chains B
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.75 | 0.89 | 39 | MG, PO4 |
| 2 | 115 | 0.75 | 0.95 | 26 | AMP, MG |
| 3 | 438 | 0.68 | 0.80 | 52 | MG |
| 4 | 61 | 0.67 | 0.95 | 25 | empty |
| 5 | 86 | 0.56 | 0.86 | 19 | empty |
Interfaces
1 interface between chains.
- B–A · 1461 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7B80 · DeAMPylation complex of monomeric FICD and AMPylated BiP (state 2) · the same entry in another collection · chain B against B, TM-score 1.00
- G3I8R9 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum chaperone bip (G3I8R9) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q9BVA6 · AlphaFold monomer V2.0 prediction for protein adenylyltransferase ficd (Q9BVA6) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 G3I8R9
- Every structure of UniProt Q9BVA6
- Elsewhere: RCSB PDB 7B80 · PDBe 7B80 · UniProt G3I8R9 · UniProt Q9BVA6
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