MolNFT v1 · #72237 · protein

Tubulin-nsc 613863: RB3 stathmin-like domain complex

3N2G · Tubulin alpha chain: “Tubulin-nsc 613863: RB3 stathmin-like domain complex”. X-ray diffraction, 4 ligands (GTP, GDP, G2N), 19 pockets (best druggability 0.83). MolNFT v1 #72237 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3N2G
Type: protein
Length: 1,826 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: D0VWZ0, D0VWY9, P63043
Ligands: GTP, GDP, G2N, MG
Pockets: 19 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 43% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha chain	protein	428	42% helix, 14% strand	D0VWZ0
B	Tubulin beta chain	protein	419	45% helix, 15% strand	D0VWY9
C	Tubulin alpha chain	protein	429	41% helix, 15% strand	D0VWZ0
D	Tubulin beta chain	protein	427	43% helix, 15% strand	D0VWY9
E	Stathmin-4	protein	123	48% helix, 7% 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
G2N · ethyl [(2R)-5-amino-2-methyl-3-phenyl-1,2-dihydropyrido[3,4-b]pyrazin-7-yl]carbamate · 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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	913	0.83	0.85	91	GTP, MG, G2N
2	890	0.83	0.85	93	GTP, MG, G2N
3	1192	0.82	0.83	134	GDP, MG
4	574	0.71	0.80	57	empty
5	552	0.69	0.79	42	empty

Interfaces

7 interfaces between chains.

A–E · 1521 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1322 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1304 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 1020 Å² buried · 8 hydrogen bonds · protein-protein
C–E · 725 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3N2G · TUBULIN-NSC 613863: 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 D0VWZ0
Every structure of UniProt D0VWY9
Every structure of UniProt P63043
Elsewhere: RCSB PDB 3N2G · PDBe 3N2G · UniProt D0VWZ0 · UniProt D0VWY9 · UniProt P63043

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