MolNFT v1 · #143823 · protein

Structure of GRP94 with a selective resorcinylic inhibitor.

6BAW · Endoplasmin: “Structure of GRP94 with a selective resorcinylic inhibitor.”. X-ray diffraction, 2 ligands (D57, PO4), 7 pockets (best druggability 0.81). MolNFT v1 #143823 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6BAW
Type: protein
Length: 846 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endoplasmin
UniProt: P41148
Ligands: D57, PO4
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Endoplasmin	protein	208	39% helix, 27% strand	P41148
A	Endoplasmin	protein	209	39% helix, 25% strand	P41148
C	Endoplasmin	protein	214	37% helix, 27% strand	P41148
D	Endoplasmin	protein	215	38% helix, 27% strand	P41148

Ligands and binding sites

D57 · dimethyl 2-[2-(1-benzyl-1H-imidazol-2-yl)ethyl]-4,6-dihydroxybenzene-1,3-dicarboxylate · ligand · 4 copies · chains B, A, C, D
PO4 · Phosphate ion · ion · 7 copies · chains B, A, C, D
EDO · 1,2-ethanediol · additive · 11 copies · chains B, A, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	961	0.81	0.83	90	D57
2	666	0.81	0.85	61	D57
3	372	0.77	0.86	31	D57
4	362	0.76	0.86	32	D57
5	297	0.56	0.77	32	empty

Interfaces

4 interfaces between chains.

B–C · 1087 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 1081 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 622 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 596 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6BAW · Structure of GRP94 with a selective resorcinylic inhibitor. · the same entry in another collection · chain D against D, TM-score 1.00
P41148 · AlphaFold monomer V2.0 prediction for endoplasmin (P41148) · a predicted model of the same protein · chain C against A, TM-score 0.86

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 6BAW · PDBe 6BAW · UniProt P41148

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