MolNFT v1 · #143470 · protein

KLP10A-amppnp in complex with a microtubule

6B0L · Tubulin alpha-1B chain: “KLP10A-amppnp in complex with a microtubule”. Electron microscopy, 5 ligands (GTP, GDP, TA1), 16 pockets (best druggability 0.87). MolNFT v1 #143470 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6B0L
Type: protein
Length: 1,238 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta chain; Kinesin-like protein KLP10A
UniProt: Q2XVP4, F2Z5B2, Q960Z0
Ligands: GTP, GDP, TA1, ANP, MG
Pockets: 16 · best druggability 0.87

Structure

electron microscopy · 3 distinct chains · 37% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	441	40% helix, 10% strand	Q2XVP4
B	Tubulin beta chain	protein	429	42% helix, 16% strand	F2Z5B2
K	Kinesin-like protein KLP10A	protein	368	26% helix, 19% strand	Q960Z0

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains A, B
GDP · Guanosine-5'-diphosphate · ligand · chains B
TA1 · Taxol · ligand · chains B
ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains K
MG · Magnesium ion · metal · 2 copies · chains A, K

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

Pockets

16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	675	0.87	0.91	76	empty
2	266	0.84	0.95	51	GTP, MG
3	225	0.83	0.95	47	empty
4	221	0.77	0.92	44	empty
5	207	0.76	0.91	50	empty

Interfaces

3 interfaces between chains.

A–B · 2032 Å² buried · 14 hydrogen bonds · protein-protein
A–K · 1012 Å² buried · 8 hydrogen bonds · protein-protein
B–K · 897 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6B0L · KLP10A-AMPPNP in complex with a microtubule · the same entry in another collection · chain A against A, TM-score 1.00
Q960Z0 · AlphaFold monomer V2.0 prediction for kinesin-like protein KLP10A (Q960Z0) · a predicted model of the same protein · chain K against A, TM-score 0.88

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 F2Z5B2
Every structure of UniProt Q960Z0
Elsewhere: RCSB PDB 6B0L · PDBe 6B0L · UniProt Q2XVP4 · UniProt F2Z5B2 · UniProt Q960Z0

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