MolNFT v1 · #169521 · protein

Tubulin-RB3_SLD in complex with colchicine

6XER · Tubulin alpha-1B chain: “Tubulin-RB3_SLD in complex with colchicine”. X-ray diffraction, 5 ligands (GTP, LOC, GDP), 20 pockets (best druggability 0.84). MolNFT v1 #169521 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6XER
Type: protein
Length: 1,827 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta chain; Stathmin-4
UniProt: Q2XVP4, A0A287AGU7, P63043
Ligands: GTP, LOC, GDP, MG, SO4
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 50% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	426	47% helix, 18% strand	Q2XVP4
B	Tubulin beta chain	protein	425	49% helix, 19% strand	A0A287AGU7
C	Tubulin alpha-1B chain	protein	426	47% helix, 18% strand	Q2XVP4
D	Tubulin beta chain	protein	430	48% helix, 19% strand	A0A287AGU7
E	Stathmin-4	protein	120	78% helix, 13% strand	P63043

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
LOC · N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide · ligand · 2 copies · chains A, B, C, D
GDP · Guanosine-5'-diphosphate · ligand · chains B
MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 3 copies · chains A, B, D

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	825	0.84	0.87	92	GTP, MG, LOC
2	922	0.83	0.85	97	GTP, MG, LOC
3	746	0.80	0.84	87	GDP
4	653	0.68	0.77	67	empty
5	301	0.68	0.83	28	empty

Interfaces

7 interfaces between chains.

A–E · 1632 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 1438 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1352 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1327 Å² buried · 19 hydrogen bonds · protein-protein
C–E · 807 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6XER · Tubulin-RB3_SLD in complex with colchicine · 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 Q2XVP4
Every structure of UniProt A0A287AGU7
Every structure of UniProt P63043
Elsewhere: RCSB PDB 6XER · PDBe 6XER · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63043

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