Research workbench
Tubulin-mtc complex
Analyse Tubulin-mtc complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NFZ
- Type
- protein
- Length
- 2,202 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, 8WB, GDP, 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 | 45% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 424 | 48% helix, 19% strand | Q6B856 |
| D | Tubulin beta-2B chain | protein | 426 | 48% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 125 | 78% helix, 14% strand | P63043 |
| F | Tubulin-tyrosine ligase | protein | 347 | 33% helix, 22% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- 8WB · 2-methoxy-5-(2,3,4-trimethoxyphenyl)cyclohepta-2,4,6-trien-1-one · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, 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 · 4 copies · chains A, E, B, C
- GOL · Glycerol · additive · chains A
- 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.86 | 0.95 | 64 | GTP, MG, 8WB |
| 2 | 392 | 0.85 | 0.94 | 68 | GTP, MG, 8WB |
| 3 | 1081 | 0.82 | 0.83 | 118 | GDP, MG |
| 4 | 166 | 0.77 | 0.94 | 31 | empty |
| 5 | 661 | 0.76 | 0.82 | 58 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1618 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1550 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1476 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 894 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 854 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5NFZ · TUBULIN-MTC 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 5NFZ · PDBe 5NFZ · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.