MolNFT v1 · #158220 · protein

Tubulin-RB3_SLD-ttl in complex with compound DJ95

6NNG · Tubulin alpha-1B chain: “Tubulin-RB3_SLD-ttl in complex with compound DJ95”. X-ray diffraction, 6 ligands (GTP, GDP, DJ9), 20 pockets (best druggability 0.86). MolNFT v1 #158220 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6NNG
Type: protein
Length: 2,187 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin tyrosine ligase
UniProt: Q2XVP4, A0A287AGU7, Q9H169, E1BQ43
Ligands: GTP, GDP, DJ9, ACP, MG, CA
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 6 distinct chains · 47% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	439	46% helix, 18% strand	Q2XVP4
B	Tubulin beta-2B chain	protein	427	49% helix, 19% strand	A0A287AGU7
C	Tubulin alpha-1B chain	protein	440	47% helix, 17% strand	Q2XVP4
D	Tubulin beta-2B chain	protein	421	48% helix, 19% strand	A0A287AGU7
E	Stathmin-4	protein	121	77% helix, 14% strand	Q9H169
F	Tubulin tyrosine ligase	protein	339	32% helix, 20% strand	E1BQ43

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
GDP · Guanosine-5'-diphosphate · ligand · chains B
DJ9 · 2-(1H-indol-6-yl)-4-(3,4,5-trimethoxyphenyl)-1H-imidazo[4,5-c]pyridine · ligand · chains A, B
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, F
CA · Calcium ion · metal · 2 copies · chains A, C
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1074	0.86	0.87	128	GTP, MG, DJ9
2	1006	0.85	0.86	123	GDP, MG
3	420	0.77	0.86	55	GTP, MG
4	131	0.76	0.95	30	empty
5	880	0.73	0.77	71	empty

Interfaces

9 interfaces between chains.

A–E · 1590 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1399 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1249 Å² buried · 11 hydrogen bonds · protein-protein
C–E · 874 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 868 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

6NNG · Tubulin-RB3_SLD-TTL in complex with compound DJ95 · the same entry in another collection · chain C against C, TM-score 1.00
Q9H169 · AlphaFold monomer V2.0 prediction for stathmin-4 (Q9H169) · a predicted model of the same protein · chain E against A, TM-score 0.76

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 Q2XVP4
Every structure of UniProt A0A287AGU7
Every structure of UniProt Q9H169
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 6NNG · PDBe 6NNG · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt Q9H169 · UniProt E1BQ43

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