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Crystal structure of human synaptonemal complex protein SYCP3

Analyse Crystal structure of human synaptonemal complex protein SYCP3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4CPC
Type: protein
Length: 1,151 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Synaptonemal complex protein 3
UniProt: Q8IZU3
Pockets: 15 · best druggability 0.70

Structure

x-ray diffraction · 7 distinct chains · 97% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Synaptonemal complex protein 3	protein	143	97% helix, 0% strand	Q8IZU3
B, F	Synaptonemal complex protein 3	protein	144	96% helix, 0% strand	Q8IZU3
C	Synaptonemal complex protein 3	protein	144	98% helix, 0% strand	Q8IZU3
D	Synaptonemal complex protein 3	protein	141	99% helix, 0% strand	Q8IZU3
E	Synaptonemal complex protein 3	protein	143	96% helix, 0% strand	Q8IZU3
G	Synaptonemal complex protein 3	protein	152	99% helix, 0% strand	Q8IZU3
H	Synaptonemal complex protein 3	protein	140	99% helix, 0% strand	Q8IZU3

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	124	0.70	0.91	20	empty
2	477	0.68	0.79	52	empty
3	123	0.68	0.90	27	empty
4	405	0.65	0.78	49	empty
5	98	0.61	0.88	22	empty

Interfaces

16 interfaces between chains.

F–G · 3051 Å² buried · 23 hydrogen bonds · protein-protein
A–D · 3040 Å² buried · 26 hydrogen bonds · protein-protein
E–H · 3038 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 3031 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 2913 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

4CPC · Crystal structure of human synaptonemal complex protein SYCP3 · the same entry in another collection · chain H against H, TM-score 1.00
Q8IZU3 · AlphaFold monomer V2.0 prediction for synaptonemal complex protein 3 (Q8IZU3) · a predicted model of the same protein · chain A against A, TM-score 0.78

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 Q8IZU3
Elsewhere: RCSB PDB 4CPC · PDBe 4CPC · UniProt Q8IZU3

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