MolNFT v1 · #21432 · protein

Tubulin-podophyllotoxin: stathmin-like domain complex

1SA1 · Tubulin alpha chain: “Tubulin-podophyllotoxin: stathmin-like domain complex”. X-ray diffraction, 4 ligands (GTP, GDP, POD), 19 pockets (best druggability 0.83). MolNFT v1 #21432 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 1SA1
Type: protein
Length: 1,845 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: P02550, P02554
Ligands: GTP, GDP, POD, MG
Pockets: 19 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 41% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha chain	protein	433	42% helix, 14% strand	P02550
B	Tubulin beta chain	protein	422	41% helix, 16% strand	P02554
C	Tubulin alpha chain	protein	430	39% helix, 12% strand	P02550
D	Tubulin beta chain	protein	426	40% helix, 15% strand	P02554
E	Stathmin 4	protein	134	49% helix, 4% strand	P02554

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C
GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
POD · 9-hydroxy-5-(3,4,5-trimethoxyphenyl)-5,8,8A,9-tetrahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol-6(5ah)-one · ligand · 2 copies · chains A, B, C, D
MG · Magnesium ion · metal · 2 copies · chains A, C

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

Pockets

19 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	1077	0.83	0.84	113	MG, GTP, POD
2	1153	0.83	0.84	111	MG, GTP, POD
3	1082	0.80	0.81	92	GDP
4	753	0.72	0.78	59	empty
5	553	0.70	0.80	52	empty

Interfaces

7 interfaces between chains.

A–E · 1763 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1215 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1184 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1057 Å² buried · 14 hydrogen bonds · protein-protein
C–E · 703 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1SA1 · Tubulin-podophyllotoxin: stathmin-like domain complex · the same entry in another collection · chain B against B, 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 0.98

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
Elsewhere: RCSB PDB 1SA1 · PDBe 1SA1 · UniProt P02550 · UniProt P02554

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