MolNFT v1 · #121595 · protein

Crystal structure of the orphan region of human ENDOGLIN/CD105

5I04 · Maltose-binding periplasmic PROTEIN,ENDOGLIN: “Crystal structure of the orphan region of human ENDOGLIN/CD105”. X-ray diffraction, 2 ligands (GLC, NAG), 10 pockets (best druggability 0.70). MolNFT v1 #121595 on GenesisL1: 3D…

PDB: 5I04
Type: protein
Length: 668 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Maltose-binding periplasmic PROTEIN,ENDOGLIN
UniProt: P0AEX9, P17813
Ligands: GLC, NAG
Pockets: 10 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Maltose-binding periplasmic PROTEIN,ENDOGLIN	protein	668	28% helix, 33% strand	P0AEX9, P17813

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
PGE · Triethylene glycol · additive · 3 copies · chains A

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

Pockets

10 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	295	0.70	0.84	32	GLC
2	424	0.69	0.80	52	empty
3	330	0.61	0.78	32	empty
4	82	0.45	0.81	15	empty
5	81	0.42	0.80	25	empty

Modifications

Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

5I04 · Crystal structure of the orphan region of human endoglin/CD105 · the same entry in another collection · chain A against A, TM-score 1.00
P17813 · AlphaFold monomer V2.0 prediction for endoglin (P17813) · a predicted model of the same protein · chain A against A, TM-score 0.46

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 P0AEX9
Every structure of UniProt P17813
Elsewhere: RCSB PDB 5I04 · PDBe 5I04 · UniProt P0AEX9 · UniProt P17813

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