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Prodomain bound BMP10 crystal form 2

Analyse Prodomain bound BMP10 crystal form 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7POJ
Type: protein
Length: 481 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bone morphogenetic protein 10
UniProt: O95393
Ligands: NAG
Pockets: 5 · best druggability 0.53

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Bone morphogenetic protein 10	protein	104	14% helix, 48% strand	O95393
C	Bone morphogenetic protein 10	protein	140	18% helix, 44% strand	O95393
D	Bone morphogenetic protein 10	protein	133	17% helix, 45% strand	O95393

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, C, D
PG4 · Tetraethylene glycol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	225	0.53	0.77	28	empty
2	128	0.43	0.76	20	empty
3	117	0.42	0.76	31	empty
4	59	0.34	0.77	13	empty
5	66	0.31	0.74	12	empty

Interfaces

3 interfaces between chains.

A–B · 1508 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 694 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 658 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7POJ · Prodomain bound BMP10 crystal form 2 · the same entry in another collection · chain D against D, TM-score 1.00
O95393 · AlphaFold monomer V2.0 prediction for bone morphogenetic protein 10 (O95393) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 O95393
Elsewhere: RCSB PDB 7POJ · PDBe 7POJ · UniProt O95393

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