Research workbench
Tubulin-dictyostatin complex
Analyse Tubulin-dictyostatin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MF4
- Type
- protein
- Length
- 2,175 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; Uncharacterized protein
- UniProt
- P81947, Q6B856, P63043, E1BQ43
- Ligands
- GTP, GDP, 7LZ, ACP, MG, CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 435 | 47% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 427 | 49% helix, 20% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 50% helix, 17% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 425 | 50% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 122 | 78% helix, 14% strand | P63043 |
| F | Uncharacterized protein | protein | 326 | 33% helix, 24% 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
- 7LZ · (3~{Z},5~{E},7~{R},8~{S},10~{S},11~{Z},13~{S},14~{R}, 15~{S},17~{S},20~{R},21~{S},22~{S})-22-[(2~{S},3~{Z})-hexa-3,5-dien-2-yl]-7,13,15,17,21-pentamethyl-8,10,14, 20-tetrakis(oxidanyl)-1-oxacyclodocosa-3,5,11-trien-2-one · ligand · 2 copies · chains B, D
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 3 copies · chains A, C, F
- GOL · Glycerol · additive · 2 copies · chains A, B, E
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.87 | 0.88 | 146 | GTP, MG |
| 2 | 1155 | 0.83 | 0.84 | 126 | GDP, MG |
| 3 | 1127 | 0.80 | 0.81 | 114 | GTP, MG |
| 4 | 67 | 0.73 | 0.98 | 21 | empty |
| 5 | 365 | 0.70 | 0.83 | 35 | MES |
Interfaces
9 interfaces between chains.
- A–E · 1589 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1426 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1307 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 953 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 825 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5MF4 · Tubulin-Dictyostatin complex · the same entry in another collection · chain C against C, 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 5MF4 · PDBe 5MF4 · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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