MolNFT v1 · #188423 · protein

CAKIP3[2-482] - AMP-pnp in complex with a dolastatin-10-stabilized tubulin ring

7TR3 · Tubulin alpha-1B chain: “CAKIP3[2-482] - AMP-pnp in complex with a dolastatin-10-stabilized tubulin ring”. Electron microscopy, 5 ligands (GTP, GDP, SR6), 18 pockets (best druggability 0.83). MolNFT v1 #188423 on GenesisL1: 3D…

PDB: 7TR3
Type: protein
Length: 1,288 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta-2B chain; Kinesin-like protein
UniProt: Q2XVP4, A0A287AGU7, A0A1D8PKA4
Ligands: GTP, GDP, SR6, ANP, MG
Pockets: 18 · best druggability 0.83

Structure

electron microscopy · 3 distinct chains · 38% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	440	41% helix, 10% strand	Q2XVP4
B	Tubulin beta-2B chain	protein	430	43% helix, 10% strand	A0A287AGU7
K	Kinesin-like protein	protein	418	29% helix, 14% strand	A0A1D8PKA4

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains A, B
GDP · Guanosine-5'-diphosphate · ligand · chains B
SR6 · dolastatin-10 · ligand · chains B
ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains K
MG · Magnesium ion · metal · chains A

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

Pockets

18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1031	0.83	0.84	84	empty
2	1089	0.80	0.81	117	GTP, MG
3	81	0.76	0.98	36	empty
4	94	0.75	0.96	14	empty
5	73	0.72	0.96	20	empty

Interfaces

3 interfaces between chains.

A–B · 1297 Å² buried · 11 hydrogen bonds · protein-protein
A–K · 1079 Å² buried · 10 hydrogen bonds · protein-protein
B–K · 697 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7TR3 · CaKip3[2-482] - AMP-PNP in complex with a dolastatin-10-stabilized tubulin ring · 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 A0A1D8PKA4
Elsewhere: RCSB PDB 7TR3 · PDBe 7TR3 · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt A0A1D8PKA4

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