MolNFT v1 · #38763 · protein

N-domain of GRP94 in complex with the 2-iodo-neca

2H8M · Endoplasmin: “N-domain of GRP94 in complex with the 2-iodo-neca”. X-ray diffraction, 1 ligand (NEI), 5 pockets (best druggability 0.62). MolNFT v1 #38763 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2H8M
Type: protein
Length: 425 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endoplasmin
UniProt: P41148
Ligands: NEI
Pockets: 5 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endoplasmin	protein	215	43% helix, 25% strand	P41148
B	Endoplasmin	protein	210	40% helix, 26% strand	P41148

Ligands and binding sites

NEI · (2S,3S,4R,5R)-5-(6-amino-2-iodo-9H-purin-9-yl)-N-ethyl-3,4-dihydroxytetrahydrofuran-2-carboxamide · ligand · 2 copies · chains A, B
PG4 · Tetraethylene glycol · additive · 9 copies · chains A, B
1PE · Pentaethylene glycol · additive · 2 copies · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	244	0.62	0.81	24	NEI, PG4
2	252	0.62	0.80	26	NEI, PG4
3	386	0.60	0.76	36	1PE
4	84	0.32	0.74	22	PG4
5	80	0.31	0.73	21	PG4

Interfaces

1 interface between chains.

A–B · 461 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

2H8M · N-Domain Of Grp94 In Complex With the 2-Iodo-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 0.88

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 2H8M · PDBe 2H8M · UniProt P41148

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