MolNFT v1 · #66234 · protein

Tubulin-ABT751: RB3 stathmin-like domain complex

3HKC · Tubulin alpha chain: “Tubulin-ABT751: RB3 stathmin-like domain complex”. X-ray diffraction, 4 ligands (GTP, GDP, E70), 19 pockets (best druggability 0.82). MolNFT v1 #66234 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3HKC
Type: protein
Length: 1,817 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha chain; Tubulin beta chain; Stathmin-4
UniProt: P63043
Ligands: GTP, GDP, E70, MG
Pockets: 19 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha chain	protein	427	41% helix, 14% strand	—
B, D	Tubulin beta chain	protein	419	44% helix, 14% strand	—
C	Tubulin alpha chain	protein	428	42% helix, 15% strand	—
E	Stathmin-4	protein	124	27% helix, 6% strand	P63043

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
E70 · N-{2-[(4-hydroxyphenyl)amino]pyridin-3-yl}-4-methoxybenzenesulfonamide · ligand · 2 copies · chains A, B, C, D
MG · Magnesium ion · metal · 3 copies · chains A, B, C, D

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

Pockets

19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	963	0.82	0.84	104	GTP, MG, E70
2	1085	0.82	0.83	119	GDP, MG
3	938	0.82	0.84	97	GTP, MG, E70
4	510	0.73	0.82	51	empty
5	658	0.71	0.79	50	empty

Interfaces

7 interfaces between chains.

A–E · 1526 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1276 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1255 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 994 Å² buried · 7 hydrogen bonds · protein-protein
C–E · 729 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3HKC · Tubulin-ABT751: RB3 stathmin-like domain 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 P63043
Elsewhere: RCSB PDB 3HKC · PDBe 3HKC · UniProt P63043

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