MolNFT v1 · #139844 · protein + DNA
Structure of a ssdna bound to the outer DNA binding site of RAD52
5XS0 · DNA repair protein RAD52 homolog: “Structure of a ssdna bound to the outer DNA binding site of RAD52”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #139844 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5XS0
- Type
- protein + DNA
- Length
- 4,069 residues
- Chains
- 26
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein RAD52 homolog; Ssdna (5'-D(*CP*CP*CP*CP*CP*C)-3'); Ssdna…
- UniProt
- P43351
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G, H, I, J, K, L, N, O, P, Q, R, S, T, U, V | DNA repair protein RAD52 homolog | protein | 184 | 39% helix, 30% strand | P43351 |
| B, M | DNA repair protein RAD52 homolog | protein | 178 | 40% helix, 29% strand | P43351 |
| W | Ssdna (5'-D(*CP*CP*CP*CP*CP*C)-3') | dna | 6 | — | — |
| X | Ssdna (5'-D(*CP*CP*CP*CP*CP*CP*CP*C)-3') | dna | 8 | — | — |
| Y | Ssdna (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3') | dna | 10 | — | — |
| Z | Ssdna (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*C)-3') | dna | 9 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 746 | 0.78 | 0.82 | 96 | empty |
| 2 | 601 | 0.76 | 0.82 | 74 | empty |
| 3 | 609 | 0.75 | 0.82 | 79 | empty |
| 4 | 592 | 0.75 | 0.82 | 75 | empty |
| 5 | 584 | 0.75 | 0.82 | 74 | empty |
Interfaces
60 interfaces between chains.
- C–D · 2714 Ų buried · 41 hydrogen bonds · protein-protein
- I–J · 2693 Ų buried · 41 hydrogen bonds · protein-protein
- N–O · 2692 Ų buried · 39 hydrogen bonds · protein-protein
- H–I · 2673 Ų buried · 39 hydrogen bonds · protein-protein
- T–U · 2673 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 5XS0 · Structure of a ssDNA bound to the outer DNA binding site of RAD52 · the same entry in another collection · chain K against K, 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 P43351
- Elsewhere: RCSB PDB 5XS0 · PDBe 5XS0 · UniProt P43351
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