Research workbench
Atomic structure of the poxvirus initially transcribing complex in conformation 2
Analyse Atomic structure of the poxvirus initially transcribing complex in conformation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AP8
- Type
- protein + DNA + RNA
- Length
- 3,824 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase 147 kda polypeptide; DNA-directed RNA polymerase…
- EC
- 2.7.7.6
- UniProt
- Q1PIV1, Q49PH2, Q49PG1, A4GDF1, Q49QC8, Q49PL6, Q1PIU7, Q49QI2, H2DZ00
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 12 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase 147 kda polypeptide (EC 2.7.7.6) | protein | 1268 | 41% helix, 15% strand | Q1PIV1 |
| B | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 1129 | 31% helix, 23% strand | Q49PH2 |
| C | DNA-directed RNA polymerase 35 kda subunit (EC 2.7.7.6) | protein | 304 | 38% helix, 21% strand | Q49PG1 |
| E | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 184 | 23% helix, 24% strand | A4GDF1 |
| F | DNA-directed RNA polymerase 19 kda subunit (EC 2.7.7.6) | protein | 103 | 60% helix, 6% strand | Q49QC8 |
| G | DNA-directed RNA polymerase 18 kda subunit (EC 2.7.7.6) | protein | 153 | 10% helix, 55% strand | Q49PL6 |
| I | Protein H4 | protein | 464 | 31% helix, 17% strand | Q1PIU7 |
| J | DNA-directed RNA polymerase 7 kda subunit (EC 2.7.7.6) | protein | 61 | 36% helix, 8% strand | Q49QI2 |
| N | Synthetic promoter DNA oligomer, non-template strand | dna | 16 | — | — |
| P | RNA (5'-R(P*AP*UP*AP*AP*A)-3') | rna | 5 | — | — |
| S | DNA-directed RNA polymerase 30 kda polypeptide (EC 2.7.7.6) | protein | 116 | 45% helix, 1% strand | H2DZ00 |
| T | Synthetic promoter DNA oligomer, template strand | dna | 21 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.86 | 0.90 | 103 | empty |
| 2 | 656 | 0.86 | 0.90 | 68 | empty |
| 3 | 682 | 0.85 | 0.88 | 91 | empty |
| 4 | 918 | 0.84 | 0.85 | 80 | empty |
| 5 | 1010 | 0.79 | 0.80 | 76 | empty |
Interfaces
31 interfaces between chains.
- A–B · 9648 Ų buried · 122 hydrogen bonds · protein-protein
- B–I · 4151 Ų buried · 28 hydrogen bonds · protein-protein
- A–I · 3637 Ų buried · 39 hydrogen bonds · protein-protein
- A–S · 3360 Ų buried · 32 hydrogen bonds · protein-protein
- A–E · 2721 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7AP8 · Atomic structure of the poxvirus initially transcribing complex in conformation 2 · 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 Q1PIV1
- Every structure of UniProt Q49PH2
- Every structure of UniProt Q49PG1
- Every structure of UniProt A4GDF1
- Every structure of UniProt Q49QC8
- Every structure of UniProt Q49PL6
- Every structure of UniProt Q1PIU7
- Every structure of UniProt Q49QI2
- Every structure of UniProt H2DZ00
- Elsewhere: RCSB PDB 7AP8 · PDBe 7AP8 · UniProt Q1PIV1 · UniProt Q49PH2 · UniProt Q49PG1 · UniProt A4GDF1 · UniProt Q49QC8 · UniProt Q49PL6 · UniProt Q1PIU7 · UniProt Q49QI2 · UniProt H2DZ00
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.