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Structural basis for specific inhibition of extracellular activation of PRO/LATENT myostatin by srk-015

Analyse Structural basis for specific inhibition of extracellular activation of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UMX
Type: protein
Length: 1,427 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GROWTH/DIFFERENTIATION factor 8; GL29H4-16 Fab light CHAIN,GL29H4-16 Fab light chain…
UniProt: O14793, P0DOY2, Q5EFE5
Pockets: 19 · best druggability 0.73

Structure

x-ray diffraction · 6 distinct chains · 12% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GROWTH/DIFFERENTIATION factor 8	protein	279	16% helix, 35% strand	O14793
L	GL29H4-16 Fab light CHAIN,GL29H4-16 Fab light chain	protein	214	9% helix, 50% strand	P0DOY2
H	GL29H4-16 Fab heavy CHAIN,GL29H4-16 Fab heavy chain	protein	226	9% helix, 50% strand	Q5EFE5
l	GL29H4-16 Fab light CHAIN,GL29H4-16 Fab light chain	protein	210	9% helix, 51% strand	P0DOY2
h	GL29H4-16 Fab heavy CHAIN,GL29H4-16 Fab heavy chain	protein	225	9% helix, 50% strand	Q5EFE5
B	GROWTH/DIFFERENTIATION factor 8	protein	273	16% helix, 37% strand	O14793

Ligands and binding sites

GOL · Glycerol · additive · chains h

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

Pockets

19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	813	0.73	0.78	91	empty
2	747	0.72	0.78	66	empty
3	59	0.70	0.96	18	empty
4	277	0.65	0.81	36	empty
5	213	0.57	0.79	37	empty

Interfaces

10 interfaces between chains.

A–B · 3757 Å² buried · 27 hydrogen bonds · protein-protein
L–H · 2092 Å² buried · 15 hydrogen bonds · protein-protein
l–h · 1863 Å² buried · 13 hydrogen bonds · protein-protein
h–B · 632 Å² buried · 10 hydrogen bonds · protein-protein
A–H · 627 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

6UMX · Structural basis for specific inhibition of extracellular activation of pro/latent… · the same entry in another collection · chain B against B, TM-score 1.00
O14793 · AlphaFold monomer V2.0 prediction for GROWTH/DIFFERENTIATION factor 8 (O14793) · a predicted model of the same protein · chain B against A, TM-score 0.72
P0DOY2 · AlphaFold monomer V2.0 prediction for immunoglobulin lambda constant 2 (P0DOY2) · a predicted model of the same protein · chain l against A, TM-score 0.49

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 O14793
Every structure of UniProt P0DOY2
Every structure of UniProt Q5EFE5
Elsewhere: RCSB PDB 6UMX · PDBe 6UMX · UniProt O14793 · UniProt P0DOY2 · UniProt Q5EFE5

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