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Structure of a growth factor precursor

Analyse Structure of a growth factor precursor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MJK
Type: protein
Length: 750 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Platelet-derived growth factor subunit a
UniProt: P04085
Pockets: 11 · best druggability 0.84

Structure

x-ray diffraction · 6 distinct chains · 16% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Platelet-derived growth factor subunit a	protein	129	14% helix, 44% strand	P04085
B	Platelet-derived growth factor subunit a	protein	124	18% helix, 48% strand	P04085
E	Platelet-derived growth factor subunit a	protein	122	16% helix, 49% strand	P04085
F	Platelet-derived growth factor subunit a	protein	125	18% helix, 45% strand	P04085
X	Platelet-derived growth factor subunit a	protein	121	14% helix, 50% strand	P04085
Y	Platelet-derived growth factor subunit a	protein	129	16% helix, 46% strand	P04085

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	766	0.84	0.87	104	empty
2	209	0.69	0.87	37	empty
3	142	0.45	0.76	23	empty
4	121	0.41	0.76	23	empty
5	117	0.41	0.76	22	empty

Interfaces

12 interfaces between chains.

A–B · 2633 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 2444 Å² buried · 20 hydrogen bonds · protein-protein
X–Y · 2305 Å² buried · 18 hydrogen bonds · protein-protein
A–E · 406 Å² buried · 1 hydrogen bond · protein-protein
B–X · 361 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

3MJK · Structure of a growth factor precursor · the same entry in another collection · chain Y against Y, TM-score 1.00
P04085 · AlphaFold monomer V2.0 prediction for platelet-derived growth factor subunit a (P04085) · a predicted model of the same protein · chain E against A, TM-score 0.98

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 P04085
Elsewhere: RCSB PDB 3MJK · PDBe 3MJK · UniProt P04085

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