Research workbench
Crystal structure of ddrb from deinococcus radiodurans bound to ssdna
Analyse Crystal structure of ddrb from deinococcus radiodurans bound to ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HQB
- Type
- protein + DNA
- Length
- 637 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-stranded DNA-binding protein ddrb; 5'-D(*TP*TP*TP*T)-3'
- UniProt
- Q9RY80
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-stranded DNA-binding protein ddrb | protein | 143 | 17% helix, 41% strand | Q9RY80 |
| B | Single-stranded DNA-binding protein ddrb | protein | 131 | 19% helix, 39% strand | Q9RY80 |
| C | Single-stranded DNA-binding protein ddrb | protein | 118 | 19% helix, 36% strand | Q9RY80 |
| D | Single-stranded DNA-binding protein ddrb | protein | 109 | 20% helix, 36% strand | Q9RY80 |
| E | Single-stranded DNA-binding protein ddrb | protein | 128 | 17% helix, 41% strand | Q9RY80 |
| M, N | 5'-D(*TP*TP*TP*T)-3' | dna | 4 | — | — |
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.79 | 0.85 | 80 | empty |
| 2 | 379 | 0.75 | 0.86 | 42 | empty |
| 3 | 224 | 0.68 | 0.86 | 32 | empty |
| 4 | 550 | 0.65 | 0.77 | 55 | empty |
| 5 | 379 | 0.59 | 0.76 | 44 | empty |
Interfaces
9 interfaces between chains.
- A–B · 903 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 739 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 695 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 684 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 662 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4HQB · Crystal structure of DdrB from Deinococcus radiodurans bound to ssDNA · the same entry in another collection · chain N against N, TM-score 1.00
- Q9RY80 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein ddrb (Q9RY80) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q9RY80
- Elsewhere: RCSB PDB 4HQB · PDBe 4HQB · UniProt Q9RY80
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