MolNFT v1 · #191236 · protein + DNA
12-mer DNA structure of exbim bound to RNase-H
8CTY · Ribonuclease H: “12-mer DNA structure of exbim bound to RNase-H”. X-ray diffraction, 2 ligands (NA, CL), 14 pockets (best druggability 0.70). MolNFT v1 #191236 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8CTY
- Type
- protein + DNA
- Length
- 1,114 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease H; DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3')
- EC
- 3.1.26.4
- UniProt
- Q9KEI9
- Ligands
- NA, CL
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 8 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease H (EC 3.1.26.4) | protein | 133 | 35% helix, 26% strand | Q9KEI9 |
| C, D | Ribonuclease H (EC 3.1.26.4) | protein | 130 | 38% helix, 27% strand | Q9KEI9 |
| E | Ribonuclease H (EC 3.1.26.4) | protein | 129 | 36% helix, 24% strand | Q9KEI9 |
| F, G | Ribonuclease H (EC 3.1.26.4) | protein | 132 | 37% helix, 26% strand | Q9KEI9 |
| H | Ribonuclease H (EC 3.1.26.4) | protein | 128 | 34% helix, 24% strand | Q9KEI9 |
| I, J, K, L | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3') | dna | 12 | — | — |
| M | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3') | dna | 9 | — | — |
| N | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OWR)P*GP*CP*G)-3') | dna | 10 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains F, M
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, E, I, J
- GOL · Glycerol · additive · 7 copies · chains B, G, C, E, K, F
- ACT · Acetate ion · additive · 3 copies · chains F, G, E, M, N
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.70 | 0.80 | 56 | GOL |
| 2 | 469 | 0.66 | 0.78 | 75 | empty |
| 3 | 357 | 0.60 | 0.77 | 41 | empty |
| 4 | 273 | 0.58 | 0.78 | 32 | empty |
| 5 | 260 | 0.54 | 0.76 | 36 | empty |
Interfaces
24 interfaces between chains.
- I–J · 725 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- K–L · 683 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- M–N · 439 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- B–C · 421 Ų buried · 5 hydrogen bonds · protein-protein
- E–L · 409 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 5 modified (nucleotide modification).
Compared structures
- 8CTY · 12-mer DNA structure of ExBIM bound to RNase-H · 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 Q9KEI9
- Elsewhere: RCSB PDB 8CTY · PDBe 8CTY · UniProt Q9KEI9
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