Research workbench
Structure of the mind complex shows a regulatory focus of yeast kinetochore assembly
Analyse Structure of the mind complex shows a regulatory focus of yeast kinetochore… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T59
- Type
- protein
- Length
- 462 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KLLA0F02343P; KLLA0E05809P; KLLA0B13629P
- UniProt
- Q6CLK3, Q6CPD1, Q6CVA1
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 6 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | KLLA0F02343P | protein | 114 | 75% helix, 4% strand | Q6CLK3 |
| B | KLLA0E05809P | protein | 90 | 86% helix, 0% strand | Q6CPD1 |
| C | KLLA0B13629P | protein | 32 | 13% helix, 13% strand | Q6CVA1 |
| D | KLLA0F02343P | protein | 101 | 76% helix, 4% strand | Q6CLK3 |
| E | KLLA0E05809P | protein | 90 | 87% helix, 0% strand | Q6CPD1 |
| F | KLLA0B13629P | protein | 35 | 11% helix, 11% strand | Q6CVA1 |
Ligands and binding sites
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 2 copies · chains A, B, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.61 | 0.83 | 23 | NHE |
| 2 | 50 | 0.46 | 0.85 | 15 | empty |
| 3 | 144 | 0.44 | 0.76 | 25 | empty |
| 4 | 88 | 0.43 | 0.79 | 17 | empty |
| 5 | 55 | 0.31 | 0.76 | 16 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2280 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 2115 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 977 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 943 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 348 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5T59 · Structure of the MIND Complex Shows a Regulatory Focus of Yeast Kinetochore Assembly · the same entry in another collection · chain A against A, 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 Q6CLK3
- Every structure of UniProt Q6CPD1
- Every structure of UniProt Q6CVA1
- Elsewhere: RCSB PDB 5T59 · PDBe 5T59 · UniProt Q6CLK3 · UniProt Q6CPD1 · UniProt Q6CVA1
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