MolNFT v1 · #169118 · protein

Tubulin-RB3_SLD-ttl in complex with compound 5L

6X1E · Tubulin alpha-1B chain: “Tubulin-RB3_SLD-ttl in complex with compound 5L”. X-ray diffraction, 6 ligands (GTP, Y5L, GDP), 20 pockets (best druggability 0.86). MolNFT v1 #169118 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6X1E
Type: protein
Length: 2,173 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin tyrosine ligase
UniProt: Q2XVP4, A0A287AGU7, P63043, E1BQ43
Ligands: GTP, Y5L, GDP, ACP, MG, CA
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 6 distinct chains · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	437	46% helix, 18% strand	Q2XVP4
B	Tubulin beta-2B chain	protein	427	47% helix, 19% strand	A0A287AGU7
C	Tubulin alpha-1B chain	protein	440	46% helix, 18% strand	Q2XVP4
D	Tubulin beta-2B chain	protein	421	49% helix, 19% strand	A0A287AGU7
E	Stathmin-4	protein	121	78% helix, 13% strand	P63043
F	Tubulin tyrosine ligase	protein	327	31% helix, 24% strand	E1BQ43

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
Y5L · 4-(2-chloro-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl)-7-methoxy-3,4-dihydroquinoxalin-2(1H)-one · ligand · 2 copies · chains A, B, C, D
GDP · Guanosine-5'-diphosphate · ligand · chains B
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
CA · Calcium ion · metal · 2 copies · chains A, C
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	350	0.86	0.95	61	GTP, MG, Y5L
2	957	0.86	0.87	120	GTP, MG, Y5L
3	1191	0.83	0.84	122	GDP, MG
4	180	0.76	0.92	34	empty
5	721	0.74	0.80	85	empty

Interfaces

9 interfaces between chains.

A–E · 1648 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1511 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1346 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 880 Å² buried · 14 hydrogen bonds · protein-protein
C–E · 839 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6X1E · Tubulin-RB3_SLD-TTL in complex with compound 5l · the same entry in another collection · chain B against B, 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
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 6X1E · PDBe 6X1E · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63043 · UniProt E1BQ43

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