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Tubulin-mtc-zampanolide complex

Analyse Tubulin-mtc-zampanolide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NG1
Type: protein
Length: 2,207 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: P81947, Q6B856, P63043, E1BQ43
Ligands: GTP, GDP, 8WB, 8WE, ZPN, ACP, MG, CA
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 5 distinct chains · 47% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Tubulin alpha-1B chain	protein	440	46% helix, 18% strand	P81947
B	Tubulin beta-2B chain	protein	420	49% helix, 20% strand	Q6B856
D	Tubulin beta-2B chain	protein	431	48% helix, 19% strand	Q6B856
E	Stathmin-4	protein	123	77% helix, 14% strand	P63043
F	Tubulin-tyrosine ligase	protein	353	32% helix, 21% strand	E1BQ43

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
8WB · 2-methoxy-5-(2,3,4-trimethoxyphenyl)cyclohepta-2,4,6-trien-1-one · ligand · 2 copies · chains A, B, C, D
8WE · (2~{Z},4~{E})-~{N}-[(~{S})-oxidanyl-[(1~{S},2~{E}, 5~{S},11~{R},17~{S},19~{R})-3,11,19-trimethyl-7,13-bis(oxidanylidene)-6,21-dioxabicyclo[15.3.1]henicos-2-en-5-yl]methyl]hexa-2,4-dienamide · ligand · chains B
ZPN · (2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide · ligand · chains D
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
CA · Calcium ion · metal · 2 copies · chains A, C
GOL · Glycerol · additive · chains B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	350	0.86	0.95	66	GTP, MG, 8WB
2	978	0.85	0.86	128	GDP, MG, GOL
3	315	0.84	0.94	46	empty
4	324	0.84	0.94	58	GTP, MG, 8WB
5	382	0.77	0.87	45	ACP, MG

Interfaces

9 interfaces between chains.

A–E · 1621 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1442 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1397 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 978 Å² buried · 17 hydrogen bonds · protein-protein
A–F · 919 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

5NG1 · TUBULIN-MTC-zampanolide 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 P81947
Every structure of UniProt Q6B856
Every structure of UniProt P63043
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 5NG1 · PDBe 5NG1 · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43

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