MolNFT v1 · #186584 · protein + DNA + RNA
RNA polymerase II elongation complex with hairpin polyamide py-im 1, scaffold 1 soaked with CTP
7RIP: “RNA polymerase II elongation complex with hairpin polyamide py-im 1, scaffold 1 soaked with CTP”. X-ray diffraction, 4 ligands (5N0, PPV, ZN), 20 pockets (best druggability 0.88). MolNFT v1 #186584 on GenesisL1: 3D structure…
- PDB
- 7RIP
- Type
- protein + DNA + RNA
- Length
- 3,601 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA; Template strand DNA; Non-template strand DNA; DNA-directed RNA polymerase II subunit…
- EC
- 2.7.7.6
- UniProt
- P04050, P08518, P16370, P20434, P20435, P20436, P27999, P22139, P38902, P40422
- Ligands
- 5N0, PPV, ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 13 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | RNA | rna | 10 | — | — |
| T | Template strand DNA | dna | 26 | — | — |
| N | Non-template strand DNA | dna | 14 | — | — |
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1384 | 42% helix, 15% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1129 | 28% helix, 26% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 267 | 24% helix, 26% strand | P16370 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 212 | 40% helix, 23% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 86 | 30% helix, 15% strand | P20435 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 133 | 0% helix, 51% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 118 | 3% helix, 30% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 65 | 43% helix, 5% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 39% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 43 | 0% helix, 26% strand | P40422 |
Ligands and binding sites
- 5N0 · 3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl-4-[(1-methyl-1H-imidazole-2-carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-pyrrole-2-carbonyl]amino}-1H-pyrrole-2-carbonyl) amino]butanoyl}amino)-1-methyl-1H-imidazole-2-carbonyl]amino}-1-methyl-1H-pyrrole-2-carbonyl)amino]-1-methyl-1H-pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]amino}propyl)(methyl) amino]propyl}carbamoyl)benzoic acid · ligand · chains T, N, A
- PPV · Pyrophosphate · ligand · chains R, A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
- MG · Magnesium ion · metal · chains R, A, B
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 | 1086 | 0.88 | 0.90 | 133 | empty |
| 2 | 1084 | 0.87 | 0.89 | 115 | empty |
| 3 | 1026 | 0.84 | 0.85 | 103 | empty |
| 4 | 543 | 0.80 | 0.86 | 48 | empty |
| 5 | 985 | 0.78 | 0.80 | 85 | empty |
Interfaces
32 interfaces between chains.
- A–B · 9548 Ų buried · 151 hydrogen bonds · protein-protein
- A–E · 2261 Ų buried · 28 hydrogen bonds · protein-protein
- C–K · 2140 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1872 Ų buried · 32 hydrogen bonds · protein-protein
- A–F · 1855 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7RIP · RNA polymerase II elongation complex with hairpin polyamide Py-Im 1, scaffold 1 soaked… · the same entry in another collection · chain R against R, 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 P04050
- Every structure of UniProt P08518
- Every structure of UniProt P16370
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- Every structure of UniProt P20436
- Every structure of UniProt P27999
- Every structure of UniProt P22139
- Every structure of UniProt P38902
- Every structure of UniProt P40422
- Elsewhere: RCSB PDB 7RIP · PDBe 7RIP · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422
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