MolNFT v1 · #52794 · protein

Kinesin-5-tubulin complex with amppnp

2WBE · Tubulin alpha-1D chain: “Kinesin-5-tubulin complex with amppnp”. Electron microscopy, 5 ligands (GTP, GDP, TA1), 17 pockets (best druggability 0.83). MolNFT v1 #52794 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2WBE
Type: protein
Length: 1,173 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1D chain; Tubulin beta-2B chain; Bipolar kinesin krp-130
UniProt: P02550, P02554, P46863
Ligands: GTP, GDP, TA1, ANP, MG
Pockets: 17 · best druggability 0.83

Structure

electron microscopy · 3 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1D chain	protein	412	44% helix, 14% strand	P02550
B	Tubulin beta-2B chain	protein	426	44% helix, 14% strand	P02554
C	Bipolar kinesin krp-130	protein	335	33% helix, 27% strand	P46863

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 C
MG · Magnesium ion · metal · 2 copies · chains A, B, C

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

Pockets

17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	213	0.83	0.96	41	MG, GTP
2	989	0.82	0.84	99	empty
3	163	0.75	0.92	34	empty
4	67	0.73	0.97	24	empty
5	213	0.58	0.80	22	empty

Interfaces

3 interfaces between chains.

A–B · 2049 Å² buried · 38 hydrogen bonds · protein-protein
B–C · 482 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 285 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2WBE · Kinesin-5-Tubulin Complex with AMPPNP · the same entry in another collection · chain A against A, TM-score 1.00
P02550 · AlphaFold monomer V2.0 prediction for tubulin alpha-1A chain (P02550) · a predicted model of the same protein · chain A against A, TM-score 0.97
P46863 · AlphaFold monomer V2.0 prediction for kinesin-like protein KLP61F (P46863) · a predicted model of the same protein · chain C against A, TM-score 0.91

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 P02550
Every structure of UniProt P02554
Every structure of UniProt P46863
Elsewhere: RCSB PDB 2WBE · PDBe 2WBE · UniProt P02550 · UniProt P02554 · UniProt P46863

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