Research workbench
12-mer DNA structure of exbim bound to rnaseh -modified ddd
Analyse 12-mer DNA structure of exbim bound to rnaseh -modified ddd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CU0
- Type
- protein + DNA
- Length
- 419 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease H; DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*(OWR)P*CP*CP*G)-3')
- EC
- 3.1.26.4
- UniProt
- Q9KEI9
- Ligands
- NA
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease H (EC 3.1.26.4) | protein | 132 | 38% helix, 25% strand | Q9KEI9 |
| B | Ribonuclease H (EC 3.1.26.4) | protein | 133 | 35% helix, 26% strand | Q9KEI9 |
| C | Ribonuclease H (EC 3.1.26.4) | protein | 130 | 36% helix, 27% strand | Q9KEI9 |
| D, E | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*(OWR)P*CP*CP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, E
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.58 | 0.82 | 30 | EDO |
| 2 | 173 | 0.54 | 0.80 | 28 | EDO, NA |
| 3 | 265 | 0.51 | 0.74 | 28 | empty |
| 4 | 127 | 0.46 | 0.78 | 16 | EDO, GOL |
| 5 | 62 | 0.34 | 0.77 | 10 | empty |
Interfaces
6 interfaces between chains.
- D–E · 571 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–B · 455 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 402 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 363 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 202 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 8CU0 · 12-mer DNA structure of ExBIM bound to RNaseH -modified DDD · the same entry in another collection · chain E against E, 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 Q9KEI9
- Elsewhere: RCSB PDB 8CU0 · PDBe 8CU0 · UniProt Q9KEI9
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