MolNFT v1 · #23520 · protein
Crystal structure of the N-domain of GRP94 lacking the charged domain in complex with neca
1U2O · Endoplasmin: “Crystal structure of the N-domain of GRP94 lacking the charged domain in complex with neca”. X-ray diffraction, 1 ligand (NEC), 5 pockets (best druggability 0.62). MolNFT v1 #23520 on GenesisL1: 3D structure, binding…
- PDB
- 1U2O
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmin
- UniProt
- P41148
- Ligands
- NEC
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endoplasmin | protein | 226 | 41% helix, 24% strand | P41148 |
Ligands and binding sites
- NEC · N-ethyl-5'-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 | 212 | 0.62 | 0.82 | 26 | NEC |
| 2 | 231 | 0.62 | 0.81 | 26 | NEC |
| 3 | 343 | 0.59 | 0.76 | 42 | 1PE |
| 4 | 86 | 0.32 | 0.74 | 22 | PG4 |
| 5 | 72 | 0.30 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 453 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1U2O · Crystal Structure Of The N-Domain Of Grp94 Lacking The Charged Domain In Complex With Neca · 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 0.82
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 1U2O · PDBe 1U2O · UniProt P41148
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