Research workbench
Crystal structure of the SIR4 H-brct domain in complex with TY5 PS1095 peptide
Analyse Crystal structure of the SIR4 H-brct domain in complex with TY5 PS1095 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QTM
- Type
- protein
- Length
- 361 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulatory protein SIR4; Ribonuclease H
- EC
- 3.1.26.4
- UniProt
- P11978, O42838
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Regulatory protein SIR4 | protein | 112 | 48% helix, 12% strand | P11978 |
| B | Regulatory protein SIR4 | protein | 114 | 53% helix, 11% strand | P11978 |
| C | Regulatory protein SIR4 | protein | 111 | 50% helix, 12% strand | P11978 |
| D, E | Ribonuclease H (EC 3.1.26.4) | protein | 7 | 0% helix, 0% strand | O42838 |
| F | Ribonuclease H (EC 3.1.26.4) | protein | 10 | 0% helix, 0% strand | O42838 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, F, B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.59 | 0.76 | 31 | empty |
| 2 | 129 | 0.45 | 0.77 | 22 | empty |
| 3 | 75 | 0.40 | 0.79 | 16 | empty |
| 4 | 61 | 0.28 | 0.74 | 13 | empty |
Interfaces
7 interfaces between chains.
- A–B · 784 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 771 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 468 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 450 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 442 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered, phosphorylation).
Compared structures
- 6QTM · Crystal structure of the Sir4 H-BRCT domain in complex with Ty5 pS1095 peptide · the same entry in another collection · chain F against F, TM-score 1.00
- P11978 · AlphaFold monomer V2.0 prediction for regulatory protein SIR4 (P11978) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P11978
- Every structure of UniProt O42838
- Elsewhere: RCSB PDB 6QTM · PDBe 6QTM · UniProt P11978 · UniProt O42838
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