Research workbench
Crystal structure of the minimal MTR4-RED1 complex (single chain) from chaetomium thermophilum
Analyse Crystal structure of the minimal MTR4-RED1 complex (single chain) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YGU
- Type
- protein
- Length
- 557 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP dependent RNA helicase (DOB1)-like protein; RED1
- UniProt
- G0RZ64, G0S1V1
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP dependent RNA helicase (DOB1)-like protein | protein | 211 | 35% helix, 21% strand | G0RZ64 |
| B | RED1 | protein | 66 | 36% helix, 3% strand | G0S1V1 |
| C | ATP dependent RNA helicase (DOB1)-like protein | protein | 215 | 36% helix, 21% strand | G0RZ64 |
| D | RED1 | protein | 65 | 32% helix, 5% strand | G0S1V1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.77 | 0.81 | 76 | empty |
| 2 | 182 | 0.57 | 0.81 | 29 | empty |
| 3 | 226 | 0.56 | 0.79 | 37 | empty |
| 4 | 57 | 0.43 | 0.82 | 18 | empty |
| 5 | 91 | 0.35 | 0.75 | 21 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1491 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1459 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 303 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 226 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 222 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6YGU · Crystal structure of the minimal Mtr4-Red1 complex (single chain) from Chaetomium… · 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 G0RZ64
- Every structure of UniProt G0S1V1
- Elsewhere: RCSB PDB 6YGU · PDBe 6YGU · UniProt G0RZ64 · UniProt G0S1V1
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