Research workbench

Sse in complex with tubulin

Analyse Sse in complex with tubulin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DBB
Type: protein
Length: 2,199 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, GDP, H1F, ACP, MG, CA
Pockets: 20 · best druggability 0.85

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	438	46% helix, 18% strand	Q2XVP4
B	Tubulin beta chain	protein	425	48% helix, 20% strand	A0A287AGU7
C	Tubulin alpha-1B chain	protein	440	46% helix, 18% strand	Q2XVP4
D	Tubulin beta chain	protein	421	49% helix, 19% strand	A0A287AGU7
E	Stathmin-4	protein	123	78% helix, 14% strand	P63042
F	Tubulin tyrosine ligase	protein	352	33% helix, 22% strand	E1BQ43

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, C, D
GDP · Guanosine-5'-diphosphate · ligand · chains B
H1F · 5-phenyl-3-(3,4,5-trimethoxyphenyl)-3,4-dihydropyrazole-2-carbothioamide · ligand · chains A, B
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains A, E, B, 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, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1032	0.85	0.86	112	GTP, MG, H1F
2	1159	0.82	0.83	119	GDP, MG
3	236	0.80	0.93	47	empty
4	645	0.76	0.82	70	GTP, MG
5	729	0.72	0.79	66	empty

Interfaces

9 interfaces between chains.

A–E · 1661 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1364 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1350 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 843 Å² buried · 14 hydrogen bonds · protein-protein
C–E · 808 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

7DBB · SSE 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 0.75

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 7DBB · PDBe 7DBB · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63042 · UniProt E1BQ43

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