Research workbench
Crystal structure of MTR4-RED1 minimal complex from chaetomium thermophilum
Analyse Crystal structure of MTR4-RED1 minimal complex from chaetomium thermophilum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YFV
- Type
- protein
- Length
- 569 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
- 8 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP dependent RNA helicase (DOB1)-like protein | protein | 212 | 36% helix, 21% strand | G0RZ64 |
| B | RED1 | protein | 79 | 41% helix, 4% strand | G0S1V1 |
| C | ATP dependent RNA helicase (DOB1)-like protein | protein | 209 | 37% helix, 22% strand | G0RZ64 |
| D | RED1 | protein | 69 | 26% helix, 4% strand | G0S1V1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.72 | 0.80 | 63 | EPE |
| 2 | 439 | 0.66 | 0.78 | 56 | empty |
| 3 | 213 | 0.60 | 0.81 | 26 | empty |
| 4 | 99 | 0.43 | 0.78 | 18 | empty |
| 5 | 132 | 0.41 | 0.75 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1625 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1618 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 368 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 337 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6YFV · Crystal structure of Mtr4-Red1 minimal complex from Chaetomium thermophilum · 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 6YFV · PDBe 6YFV · UniProt G0RZ64 · UniProt G0S1V1
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