MolNFT v1 · #128912 · protein

Crystal structure of ampylated GRP78

5O4P · 78 kda glucose-regulated protein: “Crystal structure of ampylated GRP78”. X-ray diffraction, 2 ligands (AMP, SO4), 8 pockets (best druggability 0.71). MolNFT v1 #128912 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5O4P
Type: protein
Length: 1,040 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 78 kda glucose-regulated protein
UniProt: G3I8R9
Ligands: AMP, SO4
Pockets: 8 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	78 kda glucose-regulated protein	protein	518	33% helix, 32% strand	G3I8R9
B	78 kda glucose-regulated protein	protein	522	32% helix, 32% strand	G3I8R9

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · chains B
SO4 · Sulfate ion · ion · 13 copies · chains A, B

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

Pockets

8 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	322	0.71	0.84	45	SO4
2	329	0.70	0.83	43	SO4
3	556	0.62	0.75	59	empty
4	337	0.59	0.77	56	empty
5	278	0.53	0.75	42	empty

Interfaces

1 interface between chains.

A–B · 443 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5O4P · Crystal structure of AMPylated GRP78 · the same entry in another collection · chain A against A, TM-score 1.00
G3I8R9 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum chaperone bip (G3I8R9) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 G3I8R9
Elsewhere: RCSB PDB 5O4P · PDBe 5O4P · UniProt G3I8R9

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