Research workbench
Hyperthermophile chromosomal protein SAC7D single mutant M29F in complex with DNA GCGA(UBR)CGC
Analyse Hyperthermophile chromosomal protein SAC7D single mutant M29F in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WTP
- Type
- protein + DNA
- Length
- 159 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*GP*AP*(BRU)P*CP*GP*C)-3'; DNA-binding proteins 7A/7B/7D
- UniProt
- P13123
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, E, F | 5'-D(*GP*CP*GP*AP*(BRU)P*CP*GP*C)-3' | dna | 8 | — | — |
| A | DNA-binding proteins 7A/7B/7D | protein | 63 | 27% helix, 56% strand | P13123 |
| B | DNA-binding proteins 7A/7B/7D | protein | 64 | 30% helix, 55% strand | P13123 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.65 | 0.79 | 38 | empty |
| 2 | 53 | 0.27 | 0.74 | 12 | empty |
Interfaces
8 interfaces between chains.
- E–B · 471 Ų buried · 7 hydrogen bonds · protein-nucleic
- D–A · 425 Ų buried · 1 hydrogen bond · protein-nucleic
- C–A · 424 Ų buried · 9 hydrogen bonds · protein-nucleic
- F–B · 380 Ų buried · 2 hydrogen bonds · protein-nucleic
- E–F · 376 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 1WTP · Hyperthermophile chromosomal protein SAC7D single mutant M29F in complex with DNA… · the same entry in another collection · chain B against B, TM-score 1.00
- P13123 · AlphaFold monomer V2.0 prediction for DNA-binding protein 7D (P13123) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P13123
- Elsewhere: RCSB PDB 1WTP · PDBe 1WTP · UniProt P13123
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