MolNFT v1 · #91323 · protein

Crystal structure of human ERP27

4F9Z · Endoplasmic reticulum resident protein 27: “Crystal structure of human ERP27”. X-ray diffraction, 13 pockets (best druggability 0.76). MolNFT v1 #91323 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4F9Z
Type: protein
Length: 1,095 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endoplasmic reticulum resident protein 27
UniProt: Q96DN0
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, A, B, C, E	Endoplasmic reticulum resident protein 27	protein	219	39% helix, 23% strand	Q96DN0

Ligands and binding sites

ACT · Acetate ion · additive · 13 copies · chains D, E, B, A, C
PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · chains D, B
PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A, C

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

Pockets

13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1172	0.76	0.78	93	ACT
2	955	0.75	0.78	75	PE4
3	819	0.74	0.79	75	ACT
4	420	0.69	0.80	38	PE3
5	391	0.62	0.78	44	empty

Interfaces

4 interfaces between chains.

D–E · 1059 Å² buried · 5 hydrogen bonds · protein-protein
C–E · 1033 Å² buried · 8 hydrogen bonds · protein-protein
D–B · 1029 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 965 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4F9Z · Crystal Structure of human ERp27 · the same entry in another collection · chain E against E, TM-score 1.00
Q96DN0 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum resident protein 27 (Q96DN0) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 Q96DN0
Elsewhere: RCSB PDB 4F9Z · PDBe 4F9Z · UniProt Q96DN0

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