MolNFT v1 · #170327 · protein

Fibrinogen-like globe domain of human ANGPTL2

6Y41 · Angiopoietin-related protein 2: “Fibrinogen-like globe domain of human ANGPTL2”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.86). MolNFT v1 #170327 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6Y41
Type: protein
Length: 3,483 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Angiopoietin-related protein 2
UniProt: Q9UKU9
Ligands: CA
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 7 distinct chains · 16% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Angiopoietin-related protein 2	protein	219	16% helix, 29% strand	Q9UKU9
B, D	Angiopoietin-related protein 2	protein	218	16% helix, 30% strand	Q9UKU9
F	Angiopoietin-related protein 2	protein	220	16% helix, 29% strand	Q9UKU9
H, L	Angiopoietin-related protein 2	protein	218	16% helix, 29% strand	Q9UKU9
I	Angiopoietin-related protein 2	protein	217	16% helix, 29% strand	Q9UKU9
J, M	Angiopoietin-related protein 2	protein	217	16% helix, 29% strand	Q9UKU9
K, N, O, P	Angiopoietin-related protein 2	protein	216	16% helix, 30% strand	Q9UKU9

Ligands and binding sites

CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
EDO · 1,2-ethanediol · additive · 2 copies · chains E, P, I
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains B, G, C, H

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1006	0.86	0.87	111	empty
2	890	0.82	0.85	122	empty
3	467	0.82	0.89	45	empty
4	663	0.82	0.86	57	empty
5	800	0.72	0.78	100	empty

Interfaces

33 interfaces between chains.

K–O · 559 Å² buried · 14 hydrogen bonds · protein-protein
D–L · 513 Å² buried · 4 hydrogen bonds · protein-protein
M–O · 486 Å² buried · 8 hydrogen bonds · protein-protein
J–L · 470 Å² buried · 11 hydrogen bonds · protein-protein
A–H · 461 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide (disulfide).

Compared structures

6Y41 · Fibrinogen-like globe domain of human ANGPTL2 · the same entry in another collection · chain K against K, TM-score 1.00

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 Q9UKU9
Elsewhere: RCSB PDB 6Y41 · PDBe 6Y41 · UniProt Q9UKU9

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