Research workbench
Rtx (reverse transcription xenopolymerase) in complex with a DNA duplex and dampnpp
Analyse Rtx (reverse transcription xenopolymerase) in complex with a DNA duplex and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WYA
- Type
- protein + DNA
- Length
- 798 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA strand 1; DNA strand 2
- EC
- 2.7.7.7
- UniProt
- D0VWU9
- Ligands
- DZ4, MG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 756 | 42% helix, 23% strand | D0VWU9 |
| B | DNA strand 1 | dna | 22 | — | — |
| C | DNA strand 2 | dna | 20 | — | — |
Ligands and binding sites
- DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · chains A, B, C
- MG · Magnesium ion · metal · 5 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.80 | 0.95 | 30 | empty |
| 2 | 1138 | 0.79 | 0.81 | 66 | MG |
| 3 | 1123 | 0.75 | 0.78 | 81 | TRS, MG |
| 4 | 301 | 0.63 | 0.80 | 41 | MG, DZ4 |
| 5 | 253 | 0.54 | 0.76 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1159 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–C · 858 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- A–C · 734 Ų buried · 23 hydrogen bonds · protein-nucleic
Compared structures
- 6WYA · RTX (Reverse Transcription Xenopolymerase) in complex with a DNA duplex and dAMPNPP · 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 D0VWU9
- Elsewhere: RCSB PDB 6WYA · PDBe 6WYA · UniProt D0VWU9
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