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Crystal structure of pro-TGF-beta 1

Analyse Crystal structure of pro-TGF-beta 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VQF
Type: protein
Length: 1,330 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transforming growth factor beta-1
UniProt: P07200
Ligands: NAG, BMA
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 20% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transforming growth factor beta-1	protein	335	22% helix, 35% strand	P07200
B	Transforming growth factor beta-1	protein	320	17% helix, 36% strand	P07200
C	Transforming growth factor beta-1	protein	340	21% helix, 36% strand	P07200
D	Transforming growth factor beta-1	protein	335	19% helix, 35% strand	P07200

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, C, D
BMA · beta-D-mannopyranose · sugar

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	890	0.75	0.78	107	empty
2	622	0.71	0.79	90	empty
3	369	0.57	0.75	51	empty
4	288	0.56	0.77	35	empty
5	194	0.55	0.79	30	empty

Interfaces

6 interfaces between chains.

A–B · 4586 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 4559 Å² buried · 51 hydrogen bonds · protein-protein
B–C · 381 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 353 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 26 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

5VQF · Crystal Structure of pro-TGF-beta 1 · the same entry in another collection · chain D against D, TM-score 1.00
P07200 · AlphaFold monomer V2.0 prediction for transforming growth factor beta-1 proprotein… · a predicted model of the same protein · chain B against A, TM-score 0.68

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 P07200
Elsewhere: RCSB PDB 5VQF · PDBe 5VQF · UniProt P07200

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