MolNFT v1 · #176093 · protein

Ryx in complex with tubulin

7DBA · Tubulin alpha-1B chain: “Ryx in complex with tubulin”. X-ray diffraction, 6 ligands (GTP, GDP, H1O), 20 pockets (best druggability 0.86). MolNFT v1 #176093 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7DBA
Type: protein
Length: 2,196 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta chain; Stathmin-4; Tubulin tyrosine ligase
UniProt: Q2XVP4, A0A287AGU7, P63042, E1BQ43
Ligands: GTP, GDP, H1O, MG, CA, CL
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	47% helix, 19% strand	Q2XVP4
B	Tubulin beta chain	protein	424	47% helix, 19% strand	A0A287AGU7
C	Tubulin alpha-1B chain	protein	440	47% helix, 17% strand	Q2XVP4
D	Tubulin beta chain	protein	420	49% helix, 20% strand	A0A287AGU7
E	Stathmin-4	protein	123	76% helix, 13% strand	P63042
F	Tubulin tyrosine ligase	protein	352	31% helix, 21% strand	E1BQ43

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
H1O · 2-(1-methylindol-4-yl)-7-(3,4,5-trimethoxyphenyl)-1~{H}-benzimidazole · ligand · chains A, B
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 2 copies · chains A, C
CL · Chloride ion · ion · chains A
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, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	801	0.86	0.89	91	GTP, MG, H1O
2	809	0.81	0.84	96	GDP, MG
3	1186	0.80	0.82	124	GTP, MG
4	197	0.76	0.91	39	empty
5	292	0.75	0.87	42	empty

Interfaces

9 interfaces between chains.

A–E · 1620 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 1408 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1303 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 860 Å² buried · 14 hydrogen bonds · protein-protein
C–E · 821 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

7DBA · RYX in complex with tubulin · the same entry in another collection · chain C against C, TM-score 1.00
P63042 · AlphaFold monomer V2.0 prediction for stathmin-4 (P63042) · a predicted model of the same protein · chain E against A, TM-score 0.76

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 P63042
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 7DBA · PDBe 7DBA · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63042 · UniProt E1BQ43

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