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Structure of the BUD6 flank domain in complex with actin

Analyse Structure of the BUD6 flank domain in complex with actin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WYB
Type: protein
Length: 4,739 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle; Bud site selection protein 6
UniProt: P68135, P41697
Ligands: ATP, CA
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 8 distinct chains · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, K, Q	Actin, alpha skeletal muscle	protein	357	41% helix, 18% strand	P68135
B	Bud site selection protein 6	protein	40	70% helix, 0% strand	P41697
C, E, I, M, S, U, X	Actin, alpha skeletal muscle	protein	358	41% helix, 20% strand	P68135
D, T	Bud site selection protein 6	protein	38	71% helix, 0% strand	P41697
F, H, L, N, P, R, V, Y	Bud site selection protein 6	protein	37	73% helix, 0% strand	P41697
G	Actin, alpha skeletal muscle	protein	356	40% helix, 19% strand	P68135
J	Bud site selection protein 6	protein	39	74% helix, 0% strand	P41697
O	Actin, alpha skeletal muscle	protein	355	38% helix, 18% strand	P68135

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 12 copies · chains A, C, E, G, I, K, M, O, Q, S, U, X
CA · Calcium ion · metal · 12 copies · chains A, C, E, G, I, K, M, O, Q, S, U, X

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	516	0.87	0.93	63	empty
2	894	0.85	0.87	80	empty
3	934	0.83	0.84	83	empty
4	1005	0.82	0.84	95	ATP, CA
5	551	0.80	0.86	61	empty

Interfaces

49 interfaces between chains.

M–N · 1231 Å² buried · 13 hydrogen bonds · protein-protein
X–Y · 1203 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1188 Å² buried · 14 hydrogen bonds · protein-protein
I–J · 1181 Å² buried · 10 hydrogen bonds · protein-protein
S–T · 1174 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4WYB · Structure of the Bud6 flank domain in complex with actin · the same entry in another collection · chain J against J, 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 P68135
Every structure of UniProt P41697
Elsewhere: RCSB PDB 4WYB · PDBe 4WYB · UniProt P68135 · UniProt P41697

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