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Cryo-EM structure of gmpcpp-microtubule co-polymerised with doublecortin

Analyse Cryo-EM structure of gmpcpp-microtubule co-polymerised with doublecortin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6EVW
Type: protein
Length: 5,112 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta chain
UniProt: Q2XVP4, P02554
Ligands: GTP, G2P, MG
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 2 distinct chains · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, J, C, L, A, K	Tubulin alpha-1B chain	protein	423	41% helix, 16% strand	Q2XVP4
B, F, G, D, I, H	Tubulin beta chain	protein	429	43% helix, 17% strand	P02554

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains E, G, J, F, C, I, L, D, A, H, K, B
G2P · Phosphomethylphosphonic acid guanylate ester · ligand · 6 copies · chains A, B, E, F, G, C, D, I, H
MG · Magnesium ion · metal · 12 copies · chains E, J, C, L, A, K, B, F, G, D, I, 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	379	0.85	0.93	55	G2P, MG
2	386	0.84	0.93	56	G2P, MG
3	383	0.84	0.93	56	G2P, MG
4	356	0.83	0.93	51	GTP, MG
5	347	0.83	0.92	51	GTP, MG

Interfaces

17 interfaces between chains.

J–F · 1923 Å² buried · 16 hydrogen bonds · protein-protein
E–G · 1854 Å² buried · 10 hydrogen bonds · protein-protein
L–D · 1849 Å² buried · 10 hydrogen bonds · protein-protein
C–I · 1849 Å² buried · 10 hydrogen bonds · protein-protein
A–H · 1846 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6EVW · Cryo-EM structure of GMPCPP-microtubule co-polymerised with doublecortin · the same entry in another collection · chain E against E, 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 Q2XVP4
Every structure of UniProt P02554
Elsewhere: RCSB PDB 6EVW · PDBe 6EVW · UniProt Q2XVP4 · UniProt P02554

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