Research workbench
Diabody bound to a reverse transcriptase aptamer complex
Analyse Diabody bound to a reverse transcriptase aptamer complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VUG
- Type
- protein + DNA
- Length
- 1,219 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; Reverse transcriptase P51; Light chain variable…
- EC
- 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-
- UniProt
- P03366, A0A076Q3N8
- Ligands
- SO4
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-) | protein | 532 | 32% helix, 23% strand | P03366 |
| B | Reverse transcriptase P51 (EC 2.7.7.49, 3.1.13.2, 3.1.26.13) | protein | 419 | 35% helix, 19% strand | A0A076Q3N8 |
| C | Light chain variable fragment | protein | 110 | 3% helix, 48% strand | — |
| D | Heavy chain variable fragment | protein | 124 | 2% helix, 53% strand | — |
| E | DNA (38-mer) | dna | 34 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.84 | 0.85 | 98 | empty |
| 2 | 1136 | 0.83 | 0.84 | 86 | empty |
| 3 | 966 | 0.81 | 0.82 | 101 | SO4, GOL |
| 4 | 541 | 0.71 | 0.79 | 81 | empty |
| 5 | 587 | 0.67 | 0.77 | 46 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2745 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 1746 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–D · 930 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 687 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 503 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, nucleotide modification).
Compared structures
- 6VUG · Diabody bound to a Reverse Transcriptase Aptamer Complex · 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 P03366
- Every structure of UniProt A0A076Q3N8
- Elsewhere: RCSB PDB 6VUG · PDBe 6VUG · UniProt P03366 · UniProt A0A076Q3N8
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