MolNFT v2 · #138826 · protein + DNA + RNA
Pol II elongation complex with an N6-methyladenine-containing template and a matched UMPNPP
5W51: “Pol II elongation complex with an N6-methyladenine-containing template and a matched UMPNPP”. X-ray diffraction at 3.404, 3 ligands (2KH, ZN, MG). MolNFT v2 #138826 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5W51
- Type
- protein + DNA + RNA
- Length
- 3,543 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.404
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c); SYNTHETIC CONSTRUCT
- UniProt
- P04050, P08518, P16370, P20434, P20435, P20436, P27999, P22139, P38902, P40422
- Ligands
- 2KH, ZN, MG
Structure
x-ray diffraction · resolution 3.404 · 13 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 1371 | — | P04050 |
| B | — | protein | 1089 | — | P08518 |
| C | — | protein | 266 | — | P16370 |
| E | — | protein | 213 | — | P20434 |
| F | — | protein | 84 | — | P20435 |
| H | — | protein | 130 | — | P20436 |
| I | — | protein | 115 | — | P27999 |
| J | — | protein | 65 | — | P22139 |
| K | — | protein | 114 | — | P38902 |
| L | — | protein | 44 | — | P40422 |
| T | — | dna | 29 | — | — |
| N | — | dna | 14 | — | — |
| R | — | 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.
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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