MolNFT v1 · #129214 · protein + DNA
Salinibacter ruber single-strand binding protein D17K D71K mutant
5ODP · Single-stranded DNA-binding protein: “Salinibacter ruber single-strand binding protein D17K D71K mutant”. X-ray diffraction, 1 pocket (best druggability 0.31). MolNFT v1 #129214 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5ODP
- Type
- protein + DNA
- Length
- 215 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-stranded DNA-binding protein; DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
- UniProt
- Q2S565
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-stranded DNA-binding protein | protein | 99 | 10% helix, 62% strand | Q2S565 |
| G | Single-stranded DNA-binding protein | protein | 100 | 10% helix, 59% strand | Q2S565 |
| L | DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 8 | — | — |
| M | DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 1 | — | — |
| N, P | DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 2 | — | — |
| O | DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 3 | — | — |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.31 | 0.75 | 15 | empty |
Interfaces
9 interfaces between chains.
- A–G · 1000 Ų buried · 20 hydrogen bonds · protein-protein
- G–L · 397 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–O · 386 Ų buried · 5 hydrogen bonds · protein-nucleic
- G–P · 294 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–N · 291 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 5ODP · Salinibacter ruber Single-Strand Binding protein D17K D71K mutant · the same entry in another collection · chain A against A, 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 Q2S565
- Elsewhere: RCSB PDB 5ODP · PDBe 5ODP · UniProt Q2S565
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