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Crystal structure of the gyf domain of SMY2 in complex with a proline- rich peptide from BBP/SCSF1

Analyse Crystal structure of the gyf domain of SMY2 in complex with a proline- rich… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3FMA
Type: protein
Length: 455 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein SMY2; Branchpoint-bridging protein
UniProt: P32909, Q12186
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 7 distinct chains · 31% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein SMY2	protein	81	33% helix, 22% strand	P32909
B	Protein SMY2	protein	84	33% helix, 21% strand	P32909
C	Protein SMY2	protein	86	31% helix, 22% strand	P32909
D, E	Protein SMY2	protein	85	33% helix, 21% strand	P32909
L, O, P	Branchpoint-bridging protein	protein	7	0% helix, 0% strand	Q12186
M	Branchpoint-bridging protein	protein	7	0% helix, 0% strand	Q12186
N	Branchpoint-bridging protein	protein	6	0% helix, 0% strand	Q12186

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	756	0.70	0.77	51	empty
2	235	0.65	0.83	22	empty
3	223	0.52	0.76	21	empty
4	235	0.50	0.74	21	empty
5	131	0.36	0.73	24	empty

Interfaces

14 interfaces between chains.

C–E · 1897 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 567 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 531 Å² buried · 4 hydrogen bonds · protein-protein
B–M · 396 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 364 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 modified (engineered).

Compared structures

3FMA · Crystal structure of the GYF domain of Smy2 in complex with a proline-rich peptide from… · the same entry in another collection · chain P against P, TM-score 1.00
P32909 · AlphaFold monomer V2.0 prediction for protein SMY2 (P32909) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P32909
Every structure of UniProt Q12186
Elsewhere: RCSB PDB 3FMA · PDBe 3FMA · UniProt P32909 · UniProt Q12186

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