Research workbench

Cryo-EM structure of gmpcpp-microtubule co-polymerized with EB3

Analyse Cryo-EM structure of gmpcpp-microtubule co-polymerized with EB3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3JAL
Type: protein
Length: 5,428 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta chain; Microtubule-associated protein RP/EB family…
UniProt: Q2XVP4, P02554, Q9UPY8
Ligands: GTP, G2P, MG
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 3 distinct chains · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, J, C, L, A, K	Tubulin alpha-1B chain	protein	432	47% helix, 17% strand	Q2XVP4
F, G, D, I, B, H	Tubulin beta chain	protein	429	49% helix, 20% strand	P02554
N, M	Microtubule-associated protein RP/EB family member 3	protein	131	59% helix, 0% strand	Q9UPY8

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains E, G, F, J, C, I, D, L, A, H, B, K
G2P · Phosphomethylphosphonic acid guanylate ester · ligand · 6 copies · chains E, F, G, C, D, I, A, B, H
MG · Magnesium ion · metal · 6 copies · chains E, J, C, L, A, K

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	263	0.84	0.96	44	GTP, MG
2	258	0.84	0.96	44	GTP, MG
3	263	0.84	0.95	47	GTP, MG
4	1157	0.84	0.85	110	empty
5	264	0.83	0.95	45	GTP, MG

Interfaces

25 interfaces between chains.

D–L · 1964 Å² buried · 17 hydrogen bonds · protein-protein
F–J · 1963 Å² buried · 17 hydrogen bonds · protein-protein
E–G · 1958 Å² buried · 17 hydrogen bonds · protein-protein
B–K · 1957 Å² buried · 17 hydrogen bonds · protein-protein
C–I · 1954 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

3JAL · Cryo-EM structure of GMPCPP-microtubule co-polymerized with EB3 · the same entry in another collection · chain H against H, 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
Every structure of UniProt Q9UPY8
Elsewhere: RCSB PDB 3JAL · PDBe 3JAL · UniProt Q2XVP4 · UniProt P02554 · UniProt Q9UPY8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.