MolNFT v1 · #80990 · protein + DNA
Structure of deinococcus radiodurans ssb bound to ssdna
3UDG · Single-stranded DNA-binding protein: “Structure of deinococcus radiodurans ssb bound to ssdna”. X-ray diffraction, 1 ligand (TMP), 11 pockets (best druggability 0.69). MolNFT v1 #80990 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3UDG
- Type
- protein + DNA
- Length
- 664 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-stranded DNA-binding protein; 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T…
- UniProt
- Q9RY51
- Ligands
- TMP
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-stranded DNA-binding protein | protein | 211 | 7% helix, 61% strand | Q9RY51 |
| B | Single-stranded DNA-binding protein | protein | 214 | 7% helix, 60% strand | Q9RY51 |
| C | Single-stranded DNA-binding protein | protein | 214 | 6% helix, 64% strand | Q9RY51 |
| D, E, G | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' | dna | 5 | — | — |
| F | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' | dna | 4 | — | — |
| H, I | 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' | dna | 3 | — | — |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.69 | 0.78 | 61 | empty |
| 2 | 499 | 0.62 | 0.75 | 41 | empty |
| 3 | 82 | 0.40 | 0.78 | 16 | empty |
| 4 | 73 | 0.36 | 0.77 | 14 | empty |
| 5 | 72 | 0.35 | 0.76 | 15 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1132 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 774 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–G · 721 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 712 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–I · 389 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 3UDG · Structure of Deinococcus radiodurans SSB bound to ssDNA · the same entry in another collection · chain I against I, TM-score 1.00
- Q9RY51 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein (Q9RY51) · a predicted model of the same protein · chain B 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 Q9RY51
- Elsewhere: RCSB PDB 3UDG · PDBe 3UDG · UniProt Q9RY51
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