Research workbench
Crystal structure of SGF29 tandem tudor domain in complex with a carba containing peptide
Analyse Crystal structure of SGF29 tandem tudor domain in complex with a carba… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C0M
- Type
- protein
- Length
- 359 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Saga-associated factor 29 homolog; Carba-containing peptide
- UniProt
- Q96ES7
- Ligands
- UNX, SO4
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Saga-associated factor 29 homolog | protein | 174 | 14% helix, 37% strand | Q96ES7 |
| B | Saga-associated factor 29 homolog | protein | 176 | 13% helix, 37% strand | Q96ES7 |
| C | Carba-containing peptide | protein | 5 | 0% helix, 0% strand | — |
| D | Carba-containing peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 7 copies · chains A, D, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.82 | 0.85 | 79 | UNX |
| 2 | 115 | 0.49 | 0.80 | 20 | GOL |
| 3 | 125 | 0.45 | 0.77 | 21 | UNX |
| 4 | 59 | 0.43 | 0.83 | 17 | empty |
| 5 | 93 | 0.35 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 811 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 444 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 415 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5C0M · Crystal structure of SGF29 tandem tudor domain in complex with a Carba containing peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q96ES7 · AlphaFold monomer V2.0 prediction for saga-associated factor 29 (Q96ES7) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q96ES7
- Elsewhere: RCSB PDB 5C0M · PDBe 5C0M · UniProt Q96ES7
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