MolNFT v1 · #169119 · protein

Tubulin-RB3_SLD-ttl in complex with compound 5M

6X1F · Tubulin alpha-1B chain: “Tubulin-RB3_SLD-ttl in complex with compound 5M”. X-ray diffraction, 6 ligands (GTP, Y5M, GDP), 20 pockets (best druggability 0.86). MolNFT v1 #169119 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6X1F
Type: protein
Length: 2,170 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, Y5M, GDP, ACP, MG, CA
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 6 distinct chains · 47% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	437	45% helix, 18% strand	Q2XVP4
B	Tubulin beta-2B chain	protein	427	50% helix, 19% strand	A0A287AGU7
C	Tubulin alpha-1B chain	protein	440	46% helix, 17% 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	324	32% helix, 25% strand	E1BQ43

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
Y5M · 7-methoxy-4-(2-methyl-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl)-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 · 3 copies · chains A, B, C
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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	834	0.86	0.89	104	GTP, MG, Y5M
2	566	0.84	0.90	83	GTP, MG, Y5M
3	809	0.81	0.84	91	GDP, MG
4	137	0.76	0.94	27	empty
5	829	0.72	0.78	62	empty

Interfaces

9 interfaces between chains.

A–E · 1637 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1466 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1333 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 898 Å² buried · 13 hydrogen bonds · protein-protein
C–E · 829 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6X1F · Tubulin-RB3_SLD-TTL in complex with compound 5m · 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
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 6X1F · PDBe 6X1F · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63043 · UniProt E1BQ43

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