MolNFT v1 · #188679 · protein

Crystal structure of the activin receptor type-2A ligand binding domain in complex with activin-a

7U5P: “Crystal structure of the activin receptor type-2A ligand binding domain in complex with activin-a”. X-ray diffraction, 1 ligand (NAG), 14 pockets (best druggability 0.74). MolNFT v1 #188679 on GenesisL1: 3D structure, binding sites…

PDB: 7U5P
Type: protein
Length: 808 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Activin receptor type-2A; Inhibin beta a chain
EC: 2.7.11.30
UniProt: P27037, P08476
Ligands: NAG
Pockets: 14 · best druggability 0.74

Structure

x-ray diffraction · 5 distinct chains · 11% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Activin receptor type-2A (EC 2.7.11.30)	protein	94	11% helix, 41% strand	P27037
B	Inhibin beta a chain	protein	112	12% helix, 43% strand	P08476
D	Inhibin beta a chain	protein	109	12% helix, 45% strand	P08476
F	Inhibin beta a chain	protein	107	9% helix, 48% strand	P08476
H	Inhibin beta a chain	protein	104	10% helix, 48% strand	P08476

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, E, G

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

Pockets

14 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	713	0.74	0.80	71	empty
2	589	0.73	0.81	66	empty
3	180	0.51	0.78	27	empty
4	195	0.51	0.77	25	empty
5	173	0.49	0.77	26	empty

Interfaces

8 interfaces between chains.

D–F · 1397 Å² buried · 5 hydrogen bonds · protein-protein
B–H · 1393 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 744 Å² buried · 4 hydrogen bonds · protein-protein
G–H · 736 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 689 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 38 disulfide, 7 glycan (disulfide, N-glycosylation).

Compared structures

7U5P · Crystal structure of the activin receptor type-2A ligand binding domain in complex with… · the same entry in another collection · chain H against H, TM-score 1.00
P27037 · AlphaFold monomer V2.0 prediction for activin receptor type-2A (P27037) · a predicted model of the same protein · chain G against A, TM-score 0.95

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 P27037
Every structure of UniProt P08476
Elsewhere: RCSB PDB 7U5P · PDBe 7U5P · UniProt P27037 · UniProt P08476

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