Research workbench
Structure of a thermostable group II intron reverse transcriptase with template-primer and its functional and evolutionary implications (RT/DUPLEX (se-met))
Analyse Structure of a thermostable group II intron reverse transcriptase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AR3
- Type
- protein + DNA + RNA
- Length
- 887 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gsi-iic rt; DNA; RNA
- UniProt
- E2GM63
- Ligands
- DTP, MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gsi-iic rt | protein | 418 | 55% helix, 11% strand | E2GM63 |
| B, E | DNA | dna | 11 | — | — |
| C, F | RNA | rna | 14 | — | — |
| D | Gsi-iic rt | protein | 419 | 55% helix, 11% strand | E2GM63 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.79 | 0.82 | 76 | DTP, MG |
| 2 | 1133 | 0.78 | 0.80 | 76 | DTP, MG |
| 3 | 445 | 0.72 | 0.83 | 58 | empty |
| 4 | 280 | 0.52 | 0.75 | 30 | empty |
| 5 | 110 | 0.43 | 0.78 | 16 | empty |
Interfaces
8 interfaces between chains.
- A–D · 928 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 915 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–C · 878 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 688 Ų buried · 4 hydrogen bonds · protein-nucleic
- D–E · 628 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 6AR3 · Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer… · the same entry in another collection · chain B against B, 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 E2GM63
- Elsewhere: RCSB PDB 6AR3 · PDBe 6AR3 · UniProt E2GM63
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