Research workbench
Yeast RNA polymerase I elongation complex bound to nucleotide analog gmpcpp
Analyse Yeast RNA polymerase I elongation complex bound to nucleotide analog gmpcpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HKO
- Type
- protein + DNA + RNA
- Length
- 4,227 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase I subunit RPA190; DNA-directed RNA polymerase I subunit…
- EC
- 2.7.7.6
- UniProt
- P10964, P22138, P07703, P50106, P20434, P20435, P46669, P20436, P32529, P22139, P28000, P40422, P47006, Q01080
- Ligands
- G2P, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 17 distinct chains · 28% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase I subunit RPA190 (EC 2.7.7.6) | protein | 1458 | 38% helix, 12% strand | P10964 |
| B | DNA-directed RNA polymerase I subunit RPA135 (EC 2.7.7.6) | protein | 1166 | 26% helix, 24% strand | P22138 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 304 | 23% helix, 31% strand | P07703 |
| D | DNA-directed RNA polymerase I subunit RPA14 | protein | 59 | 34% helix, 10% strand | P50106 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 34% helix, 23% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 100 | 42% helix, 16% strand | P20435 |
| G | DNA-directed RNA polymerase I subunit RPA43 | protein | 176 | 7% helix, 42% strand | P46669 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 131 | 5% helix, 54% strand | P20436 |
| I | DNA-directed RNA polymerase I subunit RPA12 | protein | 66 | 12% helix, 24% strand | P32529 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 69 | 45% helix, 1% strand | P22139 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 98 | 40% helix, 26% strand | P28000 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 44 | 0% helix, 30% strand | P40422 |
| R | RNA | rna | 9 | — | — |
| S | Non-template strand | dna | 28 | — | — |
| T | Template strand | dna | 36 | — | — |
| N | DNA-directed RNA polymerase I subunit RPA34 | protein | 140 | 6% helix, 25% strand | P47006 |
| M | DNA-directed RNA polymerase I subunit RPA49 | protein | 129 | 8% helix, 40% strand | Q01080 |
Ligands and binding sites
- G2P · Phosphomethylphosphonic acid guanylate ester · ligand · chains A, B, R, T
- ZN · Zinc ion · metal · 6 copies · chains A, B, I, J, L
- MG · Magnesium ion · metal · chains A, R
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 | 1158 | 0.82 | 0.83 | 103 | empty |
| 2 | 562 | 0.81 | 0.87 | 79 | empty |
| 3 | 804 | 0.81 | 0.84 | 86 | empty |
| 4 | 699 | 0.81 | 0.85 | 103 | empty |
| 5 | 303 | 0.81 | 0.91 | 35 | empty |
Interfaces
42 interfaces between chains.
- A–B · 9418 Ų buried · 102 hydrogen bonds · protein-protein
- A–E · 2852 Ų buried · 39 hydrogen bonds · protein-protein
- N–M · 2430 Ų buried · 37 hydrogen bonds · protein-protein
- A–F · 2281 Ų buried · 25 hydrogen bonds · protein-protein
- B–J · 2100 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6HKO · Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP · the same entry in another collection · chain C against C, 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 P10964
- Every structure of UniProt P22138
- Every structure of UniProt P07703
- Every structure of UniProt P50106
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- Every structure of UniProt P46669
- Every structure of UniProt P20436
- Every structure of UniProt P32529
- Every structure of UniProt P22139
- Every structure of UniProt P28000
- Every structure of UniProt P40422
- Every structure of UniProt P47006
- Every structure of UniProt Q01080
- Elsewhere: RCSB PDB 6HKO · PDBe 6HKO · UniProt P10964 · UniProt P22138 · UniProt P07703 · UniProt P50106 · UniProt P20434 · UniProt P20435 · UniProt P46669 · UniProt P20436 · UniProt P32529 · UniProt P22139 · UniProt P28000 · UniProt P40422 · UniProt P47006 · UniProt Q01080
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