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Crystal structure of a curved tubulin complex induced by the kinesin- 13 KIF2A

Analyse Crystal structure of a curved tubulin complex induced by the kinesin- 13 KIF2A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BBN
Type: protein
Length: 2,267 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta-2B chain; Darpin; Kinesin-like protein KIF2A
UniProt: P81947, Q6B856, O00139
Ligands: GTP, GDP, ANP, MG, PO4
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	436	41% helix, 15% strand	P81947
B, D	Tubulin beta-2B chain	protein	431	45% helix, 18% strand	Q6B856
C	Tubulin alpha-1B chain	protein	436	43% helix, 17% strand	P81947
P	Darpin	protein	155	43% helix, 0% strand	—
E	Kinesin-like protein KIF2A	protein	378	37% helix, 21% strand	O00139

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
ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains E
MG · Magnesium ion · metal · 4 copies · chains A, B, C, E
PO4 · Phosphate ion · ion · chains D

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1193	0.83	0.85	116	empty
2	908	0.80	0.82	119	GDP, MG
3	179	0.79	0.94	33	GTP, MG
4	221	0.79	0.93	37	GTP, MG
5	61	0.73	0.98	24	empty

Interfaces

8 interfaces between chains.

C–D · 1535 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1334 Å² buried · 14 hydrogen bonds · protein-protein
C–E · 1127 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 970 Å² buried · 12 hydrogen bonds · protein-protein
D–P · 862 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6BBN · Crystal structure of a curved tubulin complex induced by the kinesin-13 Kif2A · the same entry in another collection · chain C against C, TM-score 1.00
O00139 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF2A (O00139) · a predicted model of the same protein · chain E against A, TM-score 0.89

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 O00139
Elsewhere: RCSB PDB 6BBN · PDBe 6BBN · UniProt P81947 · UniProt Q6B856 · UniProt O00139

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