MolNFT v1 · #166119 · protein
Katanin hexamer in the spiral conformation in complex with substrate
6UGD · Meiotic spindle formation protein mei-1: “Katanin hexamer in the spiral conformation in complex with substrate”. Electron microscopy, 2 ligands (ATP, MG), 20 pockets (best druggability 0.82). MolNFT v1 #166119 on GenesisL1: 3D…
- PDB
- 6UGD
- Type
- protein
- Length
- 1,865 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Meiotic spindle formation protein mei-1; Polyglutamate peptide
- EC
- 5.6.1.1
- UniProt
- P34808
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 7 distinct chains · 40% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Meiotic spindle formation protein mei-1 (EC 5.6.1.1) | protein | 305 | 43% helix, 6% strand | P34808 |
| B | Meiotic spindle formation protein mei-1 (EC 5.6.1.1) | protein | 305 | 38% helix, 7% strand | P34808 |
| C | Meiotic spindle formation protein mei-1 (EC 5.6.1.1) | protein | 308 | 39% helix, 7% strand | P34808 |
| D | Meiotic spindle formation protein mei-1 (EC 5.6.1.1) | protein | 310 | 41% helix, 7% strand | P34808 |
| E | Meiotic spindle formation protein mei-1 (EC 5.6.1.1) | protein | 312 | 43% helix, 9% strand | P34808 |
| F | Meiotic spindle formation protein mei-1 (EC 5.6.1.1) | protein | 311 | 38% helix, 8% strand | P34808 |
| G | Polyglutamate peptide | protein | 14 | 0% helix, 36% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.82 | 0.83 | 109 | empty |
| 2 | 1022 | 0.79 | 0.81 | 112 | ATP, MG |
| 3 | 1093 | 0.79 | 0.80 | 94 | ATP, MG |
| 4 | 1137 | 0.79 | 0.80 | 113 | ATP, MG |
| 5 | 798 | 0.77 | 0.81 | 98 | ATP, MG |
Interfaces
14 interfaces between chains.
- D–E · 2233 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2199 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2197 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2162 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 2124 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6UGD · Katanin hexamer in the spiral conformation in complex with substrate · the same entry in another collection · chain G against G, TM-score 1.00
- P34808 · AlphaFold monomer V2.0 prediction for meiotic spindle formation protein mei-1 (P34808) · 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 P34808
- Elsewhere: RCSB PDB 6UGD · PDBe 6UGD · UniProt P34808
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