MolNFT v1 · #127084 · protein
Ustilago maydis kinesin-5 motor domain in the amppnp state bound to microtubules
5MM4: “Ustilago maydis kinesin-5 motor domain in the amppnp state bound to microtubules”. Electron microscopy, 5 ligands (ANP, GTP, TA1), 20 pockets (best druggability 0.83). MolNFT v1 #127084 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5MM4
- Type
- protein
- Length
- 1,236 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-5; Tubulin alpha-1A chain; Tubulin beta chain
- UniProt
- A0A0D1DQH0, P02550, P02554
- Ligands
- ANP, GTP, TA1, GDP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Kinesin-5 | protein | 382 | 25% helix, 15% strand | A0A0D1DQH0 |
| A | Tubulin alpha-1A chain | protein | 428 | 39% helix, 14% strand | P02550 |
| B | Tubulin beta chain | protein | 426 | 40% helix, 16% strand | P02554 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains K
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- TA1 · Taxol · ligand · chains B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains K, A
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 | 291 | 0.83 | 0.95 | 48 | GTP, MG |
| 2 | 1093 | 0.83 | 0.84 | 98 | empty |
| 3 | 104 | 0.74 | 0.95 | 20 | empty |
| 4 | 110 | 0.72 | 0.93 | 23 | empty |
| 5 | 54 | 0.69 | 0.97 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1925 Ų buried · 27 hydrogen bonds · protein-protein
- K–A · 1095 Ų buried · 17 hydrogen bonds · protein-protein
- K–B · 1057 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5MM4 · Ustilago maydis kinesin-5 motor domain in the AMPPNP state bound to microtubules · the same entry in another collection · chain K against K, TM-score 1.00
- P02550 · AlphaFold monomer V2.0 prediction for tubulin alpha-1A chain (P02550) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 A0A0D1DQH0
- Every structure of UniProt P02550
- Every structure of UniProt P02554
- Elsewhere: RCSB PDB 5MM4 · PDBe 5MM4 · UniProt A0A0D1DQH0 · UniProt P02550 · UniProt P02554
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