MolNFT v1 · #87695 · protein

Xenopus RSPO2 FU1-FU2 crystal form I

4C8V · R-spondin-2: “Xenopus RSPO2 FU1-FU2 crystal form I”. X-ray diffraction, 10 pockets (best druggability 0.58). MolNFT v1 #87695 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4C8V
Type: protein
Length: 871 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: R-spondin-2
UniProt: Q5M7L6
Pockets: 10 · best druggability 0.58

Structure

x-ray diffraction · 6 distinct chains · 0% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	R-spondin-2	protein	115	0% helix, 50% strand	Q5M7L6
B	R-spondin-2	protein	112	0% helix, 46% strand	Q5M7L6
C	R-spondin-2	protein	113	0% helix, 48% strand	Q5M7L6
D	R-spondin-2	protein	110	0% helix, 49% strand	Q5M7L6
E, F, G	R-spondin-2	protein	105	0% helix, 49% strand	Q5M7L6
H	R-spondin-2	protein	106	0% helix, 53% strand	Q5M7L6

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	332	0.58	0.77	39	empty
2	207	0.49	0.76	36	empty
3	186	0.47	0.75	26	empty
4	154	0.46	0.76	27	empty
5	102	0.36	0.74	23	empty

Interfaces

8 interfaces between chains.

F–H · 605 Å² buried · 9 hydrogen bonds · protein-protein
A–F · 542 Å² buried · 8 hydrogen bonds · protein-protein
D–F · 490 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 470 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 446 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 64 disulfide (disulfide).

Compared structures

4C8V · Xenopus RSPO2 Fu1-Fu2 crystal form I · the same entry in another collection · chain H against H, TM-score 1.00
Q5M7L6 · AlphaFold monomer V2.0 prediction for R-spondin-2 (Q5M7L6) · a predicted model of the same protein · chain D against A, TM-score 0.87

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 Q5M7L6
Elsewhere: RCSB PDB 4C8V · PDBe 4C8V · UniProt Q5M7L6

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