MolNFT v1 · #157013 · protein
Cryo-EM structure of microtubule-bound KIF7 in the amppnp state
6MLR · Tubulin alpha-1A chain: “Cryo-EM structure of microtubule-bound KIF7 in the amppnp state”. Electron microscopy, 4 ligands (GTP, GDP, TA1), 19 pockets (best druggability 0.85). MolNFT v1 #157013 on GenesisL1: 3D structure, binding…
- PDB
- 6MLR
- Type
- protein
- Length
- 1,160 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1A chain; Tubulin beta chain; Kinesin-like protein KIF7
- UniProt
- P02550, P02554, Q2M1P5
- Ligands
- GTP, GDP, TA1, ANP
- Pockets
- 19 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1A chain | protein | 411 | 43% helix, 12% strand | P02550 |
| B | Tubulin beta chain | protein | 426 | 42% helix, 15% strand | P02554 |
| C | Kinesin-like protein KIF7 | protein | 323 | 28% helix, 23% strand | Q2M1P5 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- TA1 · Taxol · ligand · chains B
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.85 | 0.86 | 115 | empty |
| 2 | 302 | 0.84 | 0.94 | 42 | GTP |
| 3 | 97 | 0.77 | 0.97 | 22 | empty |
| 4 | 132 | 0.76 | 0.94 | 32 | empty |
| 5 | 74 | 0.69 | 0.94 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1932 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1043 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 600 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6MLR · Cryo-EM structure of microtubule-bound Kif7 in the AMPPNP state · the same entry in another collection · chain A against A, 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
- Q2M1P5 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF7 (Q2M1P5) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P02550
- Every structure of UniProt P02554
- Every structure of UniProt Q2M1P5
- Elsewhere: RCSB PDB 6MLR · PDBe 6MLR · UniProt P02550 · UniProt P02554 · UniProt Q2M1P5
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