Research workbench
Amppnp bound RAD50 in complex with dsdna
Analyse Amppnp bound RAD50 in complex with dsdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W9M
- Type
- protein + DNA
- Length
- 1,610 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*GP*AP*CP*CP*GP*AP*CP*C)- 3'); DNA…
- UniProt
- Q9X1X1, Q9X1X0
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 46% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y, Z | DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*GP*AP*CP*CP*GP*AP*CP*C)- 3') | dna | 15 | — | — |
| A, G | DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*CP*AP*CP*CP*GP*AP*CP*C)- 3') | dna | 15 | — | — |
| C, I | Probable DNA double-strand break repair RAD50 ATPase, probable DNA double-strand break repair RAD50 ATPase | protein | 352 | 43% helix, 26% strand | Q9X1X1 |
| D, J | Exonuclease, putative | protein | 36 | 81% helix, 0% strand | Q9X1X0 |
| E | Probable DNA double-strand break repair RAD50 ATPase, probable DNA double-strand break repair RAD50 ATPase | protein | 351 | 42% helix, 26% strand | Q9X1X1 |
| F | Exonuclease, putative | protein | 36 | 78% helix, 0% strand | Q9X1X0 |
| K | Probable DNA double-strand break repair RAD50 ATPase, probable DNA double-strand break repair RAD50 ATPase | protein | 352 | 43% helix, 26% strand | Q9X1X1 |
| L | Exonuclease, putative | protein | 35 | 71% helix, 0% strand | Q9X1X0 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains C, E, I, K
- MG · Magnesium ion · metal · 4 copies · chains C, E, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.81 | 0.83 | 89 | ANP, MG |
| 2 | 577 | 0.75 | 0.82 | 51 | empty |
| 3 | 779 | 0.74 | 0.79 | 87 | ANP, MG |
| 4 | 354 | 0.67 | 0.81 | 58 | ANP, MG |
| 5 | 205 | 0.66 | 0.85 | 38 | ANP, MG |
Interfaces
14 interfaces between chains.
- E–F · 1247 Ų buried · 7 hydrogen bonds · protein-protein
- I–K · 1208 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 1190 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1177 Ų buried · 2 hydrogen bonds · protein-protein
- K–L · 1176 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4W9M · AMPPNP bound Rad50 in complex with dsDNA · the same entry in another collection · chain L against L, 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 Q9X1X1
- Every structure of UniProt Q9X1X0
- Elsewhere: RCSB PDB 4W9M · PDBe 4W9M · UniProt Q9X1X1 · UniProt Q9X1X0
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