MolNFT v1 · #121064 · protein

Structure of the GREM2-GDF5 inhibitory complex

5HK5 · Gremlin-2: “Structure of the GREM2-GDF5 inhibitory complex”. X-ray diffraction, 13 pockets (best druggability 0.77). MolNFT v1 #121064 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HK5
Type: protein
Length: 925 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gremlin-2; GROWTH/DIFFERENTIATION factor 5
UniProt: O88273, P43026
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Gremlin-2	protein	128	5% helix, 55% strand	O88273
F, G	Gremlin-2	protein	129	5% helix, 51% strand	O88273
H	Gremlin-2	protein	119	3% helix, 50% strand	O88273
A, B, C, D	GROWTH/DIFFERENTIATION factor 5	protein	105	18% helix, 46% strand	P43026

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1157	0.77	0.79	89	empty
2	363	0.58	0.76	41	empty
3	396	0.58	0.75	47	empty
4	192	0.56	0.80	26	empty
5	249	0.51	0.75	39	empty

Interfaces

15 interfaces between chains.

G–H · 1831 Å² buried · 37 hydrogen bonds · protein-protein
E–F · 1753 Å² buried · 36 hydrogen bonds · protein-protein
E–A · 1587 Å² buried · 19 hydrogen bonds · protein-protein
G–B · 1542 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1285 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 disulfide (disulfide).

Compared structures

5HK5 · Structure of the Grem2-GDF5 Inhibitory Complex · the same entry in another collection · chain D against D, TM-score 1.00
P43026 · AlphaFold monomer V2.0 prediction for GROWTH/DIFFERENTIATION factor 5 (P43026) · a predicted model of the same protein · chain B 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 O88273
Every structure of UniProt P43026
Elsewhere: RCSB PDB 5HK5 · PDBe 5HK5 · UniProt O88273 · UniProt P43026

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