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Structural basis for substrate selection by T7 RNA polymerase
Analyse Structural basis for substrate selection by T7 RNA polymerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S0V
- Type
- protein + DNA + RNA
- Length
- 3,564 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*G*GP*GP*AP*AP*TP*CP*GP*AP*TP*AP*TP*CP*GP*CP*CP*GP*C)- 3'…
- EC
- 2.7.7.6
- UniProt
- P00573
- Ligands
- APC, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, H, K, N | 5'-D(*G*GP*GP*AP*AP*TP*CP*GP*AP*TP*AP*TP*CP*GP*CP*CP*GP*C)- 3' | dna | 17 | — | — |
| F, I, L, O | 5'-R(*AP*AP*CP*U*GP*CP*GP*GP*CP*GP*AP*U)-3' | rna | 8 | — | — |
| G, J, M, P | 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*C)-3' | dna | 9 | — | — |
| A, B, C, D | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 857 | 53% helix, 9% strand | P00573 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 4 copies · chains E, F, A, H, I, B, K, L, C, N, O, D
- MG · Magnesium ion · metal · 8 copies · chains E, F, A, B, I, C, L, D, O
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 | 1017 | 0.81 | 0.82 | 99 | empty |
| 2 | 1048 | 0.80 | 0.82 | 89 | empty |
| 3 | 1044 | 0.78 | 0.80 | 95 | empty |
| 4 | 540 | 0.77 | 0.84 | 66 | MG, APC |
| 5 | 813 | 0.77 | 0.81 | 95 | MG, APC |
Interfaces
23 interfaces between chains.
- H–B · 1102 Ų buried · 22 hydrogen bonds · protein-nucleic
- N–D · 1054 Ų buried · 16 hydrogen bonds · protein-nucleic
- E–A · 1024 Ų buried · 13 hydrogen bonds · protein-nucleic
- K–C · 1004 Ų buried · 7 hydrogen bonds · protein-nucleic
- F–A · 684 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 1S0V · Structural basis for substrate selection by T7 RNA polymerase · the same entry in another collection · chain E against E, 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 P00573
- Elsewhere: RCSB PDB 1S0V · PDBe 1S0V · UniProt P00573
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