Research workbench
Deampylation complex of monomeric ficd and ampylated bip (state 1)
Analyse Deampylation complex of monomeric ficd and ampylated bip (state 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B7Z
- Type
- protein
- Length
- 862 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, MG
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Endoplasmic reticulum chaperone bip (EC 3.6.4.10) | protein | 522 | 32% helix, 32% strand | G3I8R9 |
| A | Protein adenylyltransferase ficd (EC 2.7.7.-, 3.1.4.-) | protein | 340 | 69% helix, 1% strand | Q9BVA6 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains B, A
- MG · Magnesium ion · metal · chains B, A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.77 | 0.87 | 53 | AMP, MG |
| 2 | 348 | 0.74 | 0.85 | 47 | empty |
| 3 | 247 | 0.67 | 0.84 | 38 | empty |
| 4 | 114 | 0.61 | 0.87 | 37 | empty |
| 5 | 132 | 0.55 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- B–A · 1450 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7B7Z · DeAMPylation complex of monomeric FICD and AMPylated BiP (state 1) · 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 7B7Z · PDBe 7B7Z · UniProt G3I8R9 · UniProt Q9BVA6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.