Research workbench
Crystal structure of the MTERF1 Y288A substitution bound to the termination sequence.
Analyse Crystal structure of the MTERF1 Y288A substitution bound to the termination… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CO0
- Type
- protein + DNA
- Length
- 368 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription termination factor 1, mitochondrial; DNA (5'…
- UniProt
- B4DPR9
- Ligands
- K
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O | Transcription termination factor 1, mitochondrial | protein | 324 | 73% helix, 0% strand | B4DPR9 |
| D | DNA (5'- D(*AP*TP*TP*AP*CP*CP*GP*GP*GP*CP*TP*CP*TP*GP*CP*CP*AP*TP*CP*TP*TP*A)- 3') | dna | 22 | — | — |
| E | DNA (5'- D(*TP*AP*AP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*CP*CP*CP*GP*GP*TP*AP*AP*T)- 3') | dna | 22 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · chains O, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.73 | 0.82 | 48 | empty |
| 2 | 194 | 0.55 | 0.80 | 21 | empty |
Interfaces
3 interfaces between chains.
- O–E · 1437 Ų buried · 29 hydrogen bonds · protein-nucleic
- O–D · 1005 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–E · 952 Ų buried · 89 hydrogen bonds · nucleic-nucleic
Compared structures
- 5CO0 · Crystal Structure of the MTERF1 Y288A substitution bound to the termination sequence. · the same entry in another collection · chain O against O, 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 B4DPR9
- Elsewhere: RCSB PDB 5CO0 · PDBe 5CO0 · UniProt B4DPR9
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