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Structure of an accessory protein of the PCW3 relaxosome

Analyse Structure of an accessory protein of the PCW3 relaxosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VFY
Type: protein
Length: 409 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tcpk
UniProt: Q1PLI2
Pockets: 3 · best druggability 0.43

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Tcpk	protein	102	46% helix, 23% strand	Q1PLI2
C	Tcpk	protein	102	45% helix, 22% strand	Q1PLI2
D	Tcpk	protein	103	44% helix, 21% strand	Q1PLI2

Pockets

3 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	74	0.43	0.80	13	empty
2	60	0.41	0.81	13	empty
3	50	0.29	0.76	12	empty

Interfaces

4 interfaces between chains.

C–D · 985 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 927 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 585 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 73 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5VFY · Structure of an accessory protein of the pCW3 relaxosome · the same entry in another collection · chain A against A, TM-score 1.00

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 Q1PLI2
Elsewhere: RCSB PDB 5VFY · PDBe 5VFY · UniProt Q1PLI2

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