MolNFT v1 · #137979 · protein + DNA + RNA
Pol II elongation complex with an N6-methyladenine-containing template and a matched umpnpp
5W51 · DNA-directed RNA polymerase II subunit RPB1: “Pol II elongation complex with an N6-methyladenine-containing template and a matched umpnpp”. X-ray diffraction, 3 ligands (2KH, ZN, MG), 20 pockets (best druggability 0.88). MolNFT v1…
- PDB
- 5W51
- Type
- protein + DNA + RNA
- Length
- 3,543 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase II subunit RPB1; DNA-directed RNA polymerase II subunit RPB2…
- EC
- 2.7.7.6
- UniProt
- P04050, P08518, P16370, P20434, P20435, P20436, P27999, P22139, P38902, P40422
- Ligands
- 2KH, ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 13 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1371 | 40% helix, 15% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1089 | 28% helix, 25% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 266 | 23% helix, 26% strand | P16370 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 213 | 37% helix, 23% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 84 | 31% helix, 15% strand | P20435 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 130 | 0% helix, 50% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 115 | 4% helix, 26% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 65 | 45% helix, 5% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 36% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 44 | 0% helix, 23% strand | P40422 |
| T | 29MER template DNA | dna | 29 | — | — |
| N | 14MER non-template DNA | dna | 14 | — | — |
| R | 9MER RNA | rna | 9 | — | — |
Ligands and binding sites
- 2KH · 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine · ligand · chains A, B, T, R
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
- MG · Magnesium ion · metal · 2 copies · chains A, R, 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 | 1033 | 0.88 | 0.90 | 133 | empty |
| 2 | 627 | 0.85 | 0.90 | 70 | empty |
| 3 | 874 | 0.85 | 0.87 | 100 | empty |
| 4 | 924 | 0.79 | 0.82 | 114 | empty |
| 5 | 1028 | 0.79 | 0.81 | 95 | empty |
Interfaces
30 interfaces between chains.
- A–B · 9610 Ų buried · 134 hydrogen bonds · protein-protein
- A–E · 2247 Ų buried · 29 hydrogen bonds · protein-protein
- C–K · 2076 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 1999 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1832 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 5W51 · Pol II elongation complex with an N6-methyladenine-containing template and a matched… · 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 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 5W51 · PDBe 5W51 · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422
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