MolNFT v1 · #154892 · protein

BNC105 in complex with tubulin

6KPP · Tubulin alpha-1B chain: “BNC105 in complex with tubulin”. X-ray diffraction, 5 ligands (GTP, DO6, GDP), 20 pockets (best druggability 0.82). MolNFT v1 #154892 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KPP
Type: protein
Length: 2,166 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta chain; Stathmin-4; Tubulin tyrosine ligase
UniProt: Q2XVP4, A0A287AGU7, P63042, E1BQ43
Ligands: GTP, DO6, GDP, MG, CA
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 47% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	438	45% helix, 18% strand	Q2XVP4
B	Tubulin beta chain	protein	429	49% helix, 18% strand	A0A287AGU7
C	Tubulin alpha-1B chain	protein	441	47% helix, 17% strand	Q2XVP4
D	Tubulin beta chain	protein	418	49% helix, 18% strand	A0A287AGU7
E	Stathmin-4	protein	123	77% helix, 13% strand	P63042
F	Tubulin tyrosine ligase	protein	317	29% helix, 19% strand	E1BQ43

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, C
DO6 · (6-methoxy-2-methyl-7-oxidanyl-1-benzofuran-3-yl)-(3,4, 5-trimethoxyphenyl)methanone · ligand · 2 copies · chains A, B, C, D
GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 2 copies · chains A, C
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains B, C, 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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1189	0.82	0.83	131	MG, GDP, GOL
2	847	0.82	0.84	103	empty
3	161	0.80	0.96	36	DO6
4	149	0.80	0.97	33	DO6
5	202	0.79	0.93	37	GTP, MG

Interfaces

9 interfaces between chains.

A–E · 1632 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1404 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1318 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 885 Å² buried · 15 hydrogen bonds · protein-protein
A–F · 834 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6KPP · BNC105 in complex with tubulin · the same entry in another collection · chain C against C, TM-score 1.00
P63042 · AlphaFold monomer V2.0 prediction for stathmin-4 (P63042) · a predicted model of the same protein · chain E against A, TM-score 0.78

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 P63042
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 6KPP · PDBe 6KPP · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63042 · UniProt E1BQ43

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