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Crystal structure of protein related to dan and cerberus (prdc)

Analyse Crystal structure of protein related to dan and cerberus (prdc) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JPH
Type: protein
Length: 438 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gremlin-2
UniProt: O88273
Ligands: GSH
Pockets: 2 · best druggability 0.39

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gremlin-2	protein	115	13% helix, 57% strand	O88273
B, D	Gremlin-2	protein	111	11% helix, 57% strand	O88273
C	Gremlin-2	protein	101	4% helix, 64% strand	O88273

Ligands and binding sites

GSH · Glutathione · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 12 copies · chains A, B, C, D
CIT · Citric acid · additive · 2 copies · chains B, D

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	82	0.39	0.77	16	GOL
2	111	0.35	0.73	14	empty

Interfaces

3 interfaces between chains.

C–D · 2025 Å² buried · 46 hydrogen bonds · protein-protein
A–B · 1966 Å² buried · 37 hydrogen bonds · protein-protein
A–C · 377 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 4 covalent (disulfide, covalent ligand).

Compared structures

4JPH · Crystal structure of Protein Related to DAN and Cerberus (PRDC) · the same entry in another collection · chain A against A, TM-score 1.00
O88273 · AlphaFold monomer V2.0 prediction for gremlin-2 (O88273) · a predicted model of the same protein · chain C against A, TM-score 0.88

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
Elsewhere: RCSB PDB 4JPH · PDBe 4JPH · UniProt O88273

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