MolNFT v1 · #54733 · protein + DNA
Crystal structure of an artificial salen-copper basepair in complex with fragment DNA polymerase I from bacillus stearothermophilus
2XY5: “Crystal structure of an artificial salen-copper basepair in complex with fragment DNA polymerase I from…”. X-ray diffraction, 5 ligands (EDN, GLC, Z9N), 11 pockets (best druggability 0.74). MolNFT v1 #54733 on GenesisL1: 3D…
- PDB
- 2XY5
- Type
- protein + DNA
- Length
- 601 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I; 5'-D(*GP*AP*CP*CP*SAYP*TP*CP*CP*CP*TP)-3'…
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- EDN, GLC, Z9N, CU1, SO4
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I (EC 2.7.7.7) | protein | 581 | 55% helix, 13% strand | E1C9K5 |
| B | 5'-D(*GP*AP*CP*CP*SAYP*TP*CP*CP*CP*TP)-3' | dna | 10 | — | — |
| C | 5'-D(*AP*GP*GP*GP*AP*SAYP*GP*GP*TP*CP)-3' | dna | 10 | — | — |
Ligands and binding sites
- EDN · Ethane-1,2-diamine · ligand · chains B, C
- GLC · alpha-D-glucopyranose · sugar · chains A
- Z9N · alpha-D-fructofuranose · sugar · chains A
- CU1 · Copper (I) ion · metal · chains B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.74 | 0.86 | 32 | empty |
| 2 | 382 | 0.68 | 0.81 | 44 | GLC, Z9N, SO4 |
| 3 | 308 | 0.60 | 0.78 | 34 | empty |
| 4 | 110 | 0.49 | 0.80 | 22 | empty |
| 5 | 114 | 0.46 | 0.79 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 832 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 738 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 444 Ų buried · 38 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nucleotide modification).
Compared structures
- 2XY5 · Crystal structure of an artificial salen-copper basepair in complex with fragment 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 E1C9K5
- Elsewhere: RCSB PDB 2XY5 · PDBe 2XY5 · UniProt E1C9K5
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