Research workbench
Crystal structure of ddrb bound to 30B ssdna
Analyse Crystal structure of ddrb bound to 30B ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NOE
- Type
- protein + DNA
- Length
- 712 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-stranded DNA-binding protein ddrb; 5'-D(*TP*TP*GP*CP*GP*CP*TP*TP*GP*CP*GP*CP*TP*TP*…
- UniProt
- Q9RY80
- Ligands
- CA
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 20% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-stranded DNA-binding protein ddrb | protein | 139 | 21% helix, 39% strand | Q9RY80 |
| B | Single-stranded DNA-binding protein ddrb | protein | 134 | 21% helix, 40% strand | Q9RY80 |
| C | Single-stranded DNA-binding protein ddrb | protein | 134 | 21% helix, 38% strand | Q9RY80 |
| D | Single-stranded DNA-binding protein ddrb | protein | 133 | 19% helix, 38% strand | Q9RY80 |
| E | Single-stranded DNA-binding protein ddrb | protein | 142 | 20% helix, 38% strand | Q9RY80 |
| F | 5'-D(*TP*TP*GP*CP*GP*CP*TP*TP*GP*CP*GP*CP*TP*TP*GP*CP*GP*CP *TP*TP*GP*CP*GP*CP*TP*TP*GP*CP*GP*CP)-3' | dna | 30 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.77 | 0.83 | 77 | empty |
| 2 | 583 | 0.77 | 0.84 | 77 | empty |
| 3 | 614 | 0.76 | 0.82 | 79 | empty |
| 4 | 796 | 0.75 | 0.80 | 81 | empty |
| 5 | 552 | 0.74 | 0.82 | 70 | empty |
Interfaces
10 interfaces between chains.
- C–D · 944 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 893 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 869 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 857 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 843 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
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 4NOE · PDBe 4NOE · UniProt Q9RY80
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