Research workbench
N-domain of GRP94 in complex with the novel ligand N-(2-AMINO)ETHYL carboxyamido adenosine
Analyse N-domain of GRP94 in complex with the novel ligand N-(2-AMINO)ETHYL… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HCH
- Type
- protein
- Length
- 439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmin
- UniProt
- P41148
- Ligands
- N5A
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmin | protein | 221 | 43% helix, 24% strand | P41148 |
| B | Endoplasmin | protein | 218 | 42% helix, 24% strand | P41148 |
Ligands and binding sites
- N5A · 5'-N-[(2-amino)ethyl carboxamido] adenosine · ligand · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.60 | 0.80 | 25 | N5A |
| 2 | 219 | 0.59 | 0.80 | 30 | N5A |
| 3 | 328 | 0.59 | 0.77 | 32 | 1PE |
| 4 | 79 | 0.31 | 0.74 | 22 | PG4 |
| 5 | 82 | 0.31 | 0.73 | 20 | PG4 |
Interfaces
1 interface between chains.
- A–B · 458 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2HCH · N-Domain Of Grp94 In Complex With the Novel Ligand N-(2-amino)ethyl Carboxyamido Adenosine · the same entry in another collection · chain A against A, TM-score 1.00
- P41148 · AlphaFold monomer V2.0 prediction for endoplasmin (P41148) · a predicted model of the same protein · chain B against A, TM-score 0.84
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 P41148
- Elsewhere: RCSB PDB 2HCH · PDBe 2HCH · UniProt P41148
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