Research workbench
Crystal structure of the SIR4 H-brct domain in complex with UBP10 PT123 peptide
Analyse Crystal structure of the SIR4 H-brct domain in complex with UBP10 PT123 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RR0
- Type
- protein
- Length
- 868 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulatory protein SIR4; Ubiquitin carboxyl-terminal hydrolase 10
- EC
- 3.4.19.12
- UniProt
- P11978, P53874
- Ligands
- CL
- Pockets
- 14 · best druggability 0.68
Structure
x-ray diffraction · 12 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Regulatory protein SIR4 | protein | 116 | 48% helix, 12% strand | P11978 |
| B | Regulatory protein SIR4 | protein | 118 | 51% helix, 12% strand | P11978 |
| C | Regulatory protein SIR4 | protein | 115 | 51% helix, 10% strand | P11978 |
| D | Regulatory protein SIR4 | protein | 111 | 54% helix, 13% strand | P11978 |
| E | Regulatory protein SIR4 | protein | 113 | 50% helix, 11% strand | P11978 |
| F | Regulatory protein SIR4 | protein | 113 | 51% helix, 11% strand | P11978 |
| G | Regulatory protein SIR4 | protein | 112 | 52% helix, 11% strand | P11978 |
| H, M | Ubiquitin carboxyl-terminal hydrolase 10 (EC 3.4.19.12) | protein | 10 | 0% helix, 0% strand | P53874 |
| I | Ubiquitin carboxyl-terminal hydrolase 10 (EC 3.4.19.12) | protein | 11 | 0% helix, 0% strand | P53874 |
| J, K | Ubiquitin carboxyl-terminal hydrolase 10 (EC 3.4.19.12) | protein | 9 | 0% helix, 0% strand | P53874 |
| L | Ubiquitin carboxyl-terminal hydrolase 10 (EC 3.4.19.12) | protein | 12 | 0% helix, 0% strand | P53874 |
| N | Ubiquitin carboxyl-terminal hydrolase 10 (EC 3.4.19.12) | protein | 9 | 0% helix, 0% strand | P53874 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.68 | 0.78 | 52 | empty |
| 2 | 549 | 0.66 | 0.77 | 43 | empty |
| 3 | 515 | 0.66 | 0.77 | 43 | empty |
| 4 | 523 | 0.61 | 0.74 | 50 | empty |
| 5 | 341 | 0.57 | 0.76 | 28 | empty |
Interfaces
23 interfaces between chains.
- F–G · 788 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 782 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 758 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 738 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 722 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (phosphorylation).
Compared structures
- 6RR0 · Crystal structure of the Sir4 H-BRCT domain in complex with Ubp10 pT123 peptide · the same entry in another collection · chain K against K, 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 P11978
- Every structure of UniProt P53874
- Elsewhere: RCSB PDB 6RR0 · PDBe 6RR0 · UniProt P11978 · UniProt P53874
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