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Crystal structure of myova-gtd

Analyse Crystal structure of myova-gtd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WB8
Type: protein
Length: 2,861 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Unconventional myosin-va
UniProt: Q99104
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 7 distinct chains · 65% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Unconventional myosin-va	protein	362	65% helix, 1% strand	Q99104
B	Unconventional myosin-va	protein	348	64% helix, 1% strand	Q99104
C, F	Unconventional myosin-va	protein	359	66% helix, 1% strand	Q99104
D	Unconventional myosin-va	protein	360	65% helix, 2% strand	Q99104
E	Unconventional myosin-va	protein	361	66% helix, 1% strand	Q99104
G	Unconventional myosin-va	protein	360	65% helix, 2% strand	Q99104
H	Unconventional myosin-va	protein	352	66% helix, 0% strand	Q99104

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 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	1018	0.82	0.83	96	EDO
2	1055	0.78	0.80	120	EDO
3	948	0.75	0.78	75	EDO
4	52	0.70	0.97	19	empty
5	167	0.51	0.78	27	empty

Interfaces

10 interfaces between chains.

A–C · 878 Å² buried · 10 hydrogen bonds · protein-protein
D–G · 870 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 861 Å² buried · 11 hydrogen bonds · protein-protein
B–H · 787 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 503 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3WB8 · Crystal Structure of MyoVa-GTD · the same entry in another collection · chain H against H, TM-score 1.00
Q99104 · AlphaFold monomer V2.0 prediction for unconventional myosin-va (Q99104) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q99104
Elsewhere: RCSB PDB 3WB8 · PDBe 3WB8 · UniProt Q99104

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