MolNFT v1 · #138555 · protein

Structure of GRP94 N-terminal domain bound to resorcinylic inhibitor bnim.

5WMT · Endoplasmin: “Structure of GRP94 N-terminal domain bound to resorcinylic inhibitor bnim.”. X-ray diffraction, 2 ligands (9QY, MG), 9 pockets (best druggability 0.82). MolNFT v1 #138555 on GenesisL1: 3D structure, binding sites and…

PDB: 5WMT
Type: protein
Length: 845 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endoplasmin
UniProt: P41148
Ligands: 9QY, MG
Pockets: 9 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Endoplasmin	protein	210	37% helix, 26% strand	P41148
B	Endoplasmin	protein	213	40% helix, 26% strand	P41148
C	Endoplasmin	protein	212	42% helix, 26% strand	P41148

Ligands and binding sites

9QY · methyl 2-[2-(1-benzyl-1H-imidazol-2-yl)ethyl]-3-chloro-4,6-dihydroxybenzoate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 2 copies · chains B, C
EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	960	0.82	0.83	80	9QY
2	1166	0.81	0.82	97	9QY
3	351	0.79	0.89	32	9QY
4	342	0.78	0.88	31	9QY
5	64	0.35	0.77	9	empty

Interfaces

4 interfaces between chains.

A–C · 1124 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 1106 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 669 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 637 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5WMT · Structure of GRP94 N-terminal Domain bound to resorcinylic inhibitor BnIm. · the same entry in another collection · chain C against C, TM-score 1.00
P41148 · AlphaFold monomer V2.0 prediction for endoplasmin (P41148) · a predicted model of the same protein · chain D against A, TM-score 0.87

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 5WMT · PDBe 5WMT · UniProt P41148

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