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MAL3 ch domain homology model and mammalian tubulin (2XRP) docked into the 8.6-ångström cryo-EM MAP of MAL3-gtpgammas-microtubules
Analyse MAL3 ch domain homology model and mammalian tubulin (2XRP) docked into the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ABO
- Type
- protein
- Length
- 3,537 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin beta chain; Tubulin alpha-1A chain; Microtubule integrity protein MAL3
- EC
- 3.6.5.6
- UniProt
- Q10113
- Ligands
- GSP, GTP
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Tubulin beta chain (EC 3.6.5.6) | protein | 426 | 44% helix, 14% strand | — |
| B, D, F, H | Tubulin alpha-1A chain (EC 3.6.5.6) | protein | 429 | 42% helix, 14% strand | — |
| I | Microtubule integrity protein MAL3 | protein | 117 | 63% helix, 0% strand | Q10113 |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 4 copies · chains A, B, C, E, F, G
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.83 | 0.96 | 41 | GTP |
| 2 | 222 | 0.82 | 0.96 | 39 | GTP |
| 3 | 224 | 0.82 | 0.96 | 43 | GTP |
| 4 | 235 | 0.82 | 0.95 | 40 | GTP |
| 5 | 204 | 0.80 | 0.94 | 39 | GSP |
Interfaces
14 interfaces between chains.
- B–C · 1762 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1724 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1714 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1687 Ų buried · 18 hydrogen bonds · protein-protein
- F–G · 1683 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4ABO · Mal3 CH domain homology model and mammalian tubulin (2XRP) docked into the 8.6-Angstrom… · the same entry in another collection · chain I against I, TM-score 1.00
- Q10113 · AlphaFold monomer V2.0 prediction for microtubule integrity protein MAL3 (Q10113) · a predicted model of the same protein · chain I against A, TM-score 0.97
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 Q10113
- Elsewhere: RCSB PDB 4ABO · PDBe 4ABO · UniProt Q10113
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