MolNFT v1 · #152636 · protein + DNA
The structure of udgx in complex with single-stranded DNA
6IOD · Phage SPO1 DNA polymerase-related protein: “The structure of udgx in complex with single-stranded DNA”. X-ray diffraction, 2 ligands (ORP, SF4), 5 pockets (best druggability 0.83). MolNFT v1 #152636 on GenesisL1: 3D structure…
- PDB
- 6IOD
- Type
- protein + DNA
- Length
- 430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phage SPO1 DNA polymerase-related protein; DNA
- EC
- 2.7.7.7
- UniProt
- I7F541
- Ligands
- ORP, SF4
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phage SPO1 DNA polymerase-related protein (EC 2.7.7.7) | protein | 212 | 42% helix, 13% strand | I7F541 |
| B | Phage SPO1 DNA polymerase-related protein (EC 2.7.7.7) | protein | 197 | 46% helix, 14% strand | I7F541 |
| C | DNA | dna | 10 | — | — |
| D | DNA | dna | 11 | — | — |
Ligands and binding sites
- ORP · 2-deoxy-5-phosphono-ribose · ligand · 2 copies · chains A, C, B, D
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.83 | 0.84 | 95 | ORP |
| 2 | 103 | 0.61 | 0.88 | 26 | ORP |
| 3 | 110 | 0.42 | 0.77 | 16 | empty |
| 4 | 84 | 0.37 | 0.77 | 18 | empty |
| 5 | 65 | 0.30 | 0.74 | 12 | empty |
Interfaces
4 interfaces between chains.
- A–C · 659 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–D · 611 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 543 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 54 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6IOD · The structure of UdgX in complex with single-stranded DNA · 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 I7F541
- Elsewhere: RCSB PDB 6IOD · PDBe 6IOD · UniProt I7F541
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