MolNFT v1 · #190927 · protein

Tubulin-todalam-vinblastine-complex

7Z7D · Tubulin alpha-1B chain: “Tubulin-todalam-vinblastine-complex”. X-ray diffraction, 7 ligands (GTP, GDP, VLB), 20 pockets (best druggability 0.83). MolNFT v1 #190927 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7Z7D
Type: protein
Length: 2,190 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
UniProt: P81947, Q6B856, P63043, E1BQ43
Ligands: GTP, GDP, VLB, 4I2, ACP, MG, CA
Pockets: 20 · best druggability 0.83

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	46% helix, 18% strand	P81947
B	Tubulin beta-2B chain	protein	429	47% helix, 19% strand	Q6B856
C	Tubulin alpha-1B chain	protein	440	48% helix, 18% strand	P81947
D	Tubulin beta-2B chain	protein	421	49% helix, 19% strand	Q6B856
E	Stathmin-4	protein	122	78% helix, 13% strand	P63043
F	Tubulin beta-2B chain	protein	341	32% 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
VLB · (2alpha,2'beta,3beta,4alpha,5beta)-vincaleukoblastine · ligand · chains B, C
4I2 · N-(4-{2-[3-(trifluoromethyl)anilino]-1,3-thiazol-4-yl}phenyl)acetamide · ligand · chains B, C
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
CA · Calcium ion · metal · 4 copies · chains A, B, C, E
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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	989	0.83	0.84	113	GDP, MG, VLB, 4I2
2	1022	0.80	0.82	108	GTP, MG
3	995	0.79	0.81	93	ACP, MG
4	156	0.78	0.95	29	empty
5	424	0.77	0.86	52	GTP, MG

Interfaces

9 interfaces between chains.

A–E · 1591 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1427 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1408 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 953 Å² buried · 21 hydrogen bonds · protein-protein
C–E · 829 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7Z7D · Tubulin-Todalam-Vinblastine-complex · 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 P81947
Every structure of UniProt Q6B856
Every structure of UniProt P63043
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 7Z7D · PDBe 7Z7D · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43

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