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Single stranded DNA binding protein and ssdna complex
Analyse Single stranded DNA binding protein and ssdna complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EQQ
- Type
- protein + RNA
- Length
- 467 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*(5MU)P*(5MU)P*(5MU))-3'; Single stranded DNA binding protein
- UniProt
- P02339
- Ligands
- 5MU
- Pockets
- 13 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | 5'-R(*(5MU)P*(5MU)P*(5MU))-3' | rna | 3 | — | — |
| A, C | Single stranded DNA binding protein | protein | 114 | 9% helix, 46% strand | P02339 |
| B | Single stranded DNA binding protein | protein | 120 | 8% helix, 45% strand | P02339 |
| D | Single stranded DNA binding protein | protein | 116 | 9% helix, 41% strand | P02339 |
Ligands and binding sites
- 5MU · 5-methyluridine 5'-monophosphate · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.63 | 0.78 | 56 | empty |
| 2 | 55 | 0.62 | 0.93 | 17 | empty |
| 3 | 212 | 0.58 | 0.80 | 29 | empty |
| 4 | 244 | 0.53 | 0.76 | 27 | empty |
| 5 | 132 | 0.46 | 0.78 | 20 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1290 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1239 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 444 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 410 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 338 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 1EQQ · Single stranded DNA binding protein and ssdna complex · the same entry in another collection · chain M against M, 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 P02339
- Elsewhere: RCSB PDB 1EQQ · PDBe 1EQQ · UniProt P02339
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