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Crystal structure of vimentin coil 1B packed in a high-order filamentous form

Analyse Crystal structure of vimentin coil 1B packed in a high-order filamentous form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WHF
Type: protein
Length: 683 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vimentin
UniProt: P08670
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 8 distinct chains · 96% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vimentin	protein	86	95% helix, 0% strand	P08670
B	Vimentin	protein	82	96% helix, 0% strand	P08670
C	Vimentin	protein	88	98% helix, 0% strand	P08670
D	Vimentin	protein	85	96% helix, 0% strand	P08670
E	Vimentin	protein	86	92% helix, 0% strand	P08670
F	Vimentin	protein	84	98% helix, 0% strand	P08670
G	Vimentin	protein	88	97% helix, 0% strand	P08670
H	Vimentin	protein	84	98% helix, 0% strand	P08670

Ligands and binding sites

GOL · Glycerol · additive · chains G

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1037	0.74	0.77	92	empty
2	768	0.66	0.74	62	empty
3	104	0.34	0.73	17	empty
4	58	0.28	0.74	12	empty
5	58	0.26	0.72	15	empty

Interfaces

17 interfaces between chains.

C–D · 2391 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 2335 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 2241 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 2175 Å² buried · 9 hydrogen bonds · protein-protein
E–H · 599 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5WHF · Crystal structure of vimentin coil 1B packed in a high-order filamentous form · 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 P08670
Elsewhere: RCSB PDB 5WHF · PDBe 5WHF · UniProt P08670

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