Research workbench
RNA polymerase II from komagataella pastoris (type-3 crystal)
Analyse RNA polymerase II from komagataella pastoris (type-3 crystal) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X51
- Type
- protein
- Length
- 7,636 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit; DNA-directed RNA polymerase subunit beta; RNA…
- EC
- 2.7.7.6
- UniProt
- C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, C4QWA8
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 15 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 1384 | 38% helix, 14% strand | C4R4Y0 |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1073 | 27% helix, 20% strand | C4QZQ7 |
| C, O | RNA polymerase II third largest subunit B44, part of central core | protein | 265 | 23% helix, 17% strand | C4R7L2 |
| D | RNA polymerase II subunit B32 | protein | 163 | 42% helix, 7% strand | C4R2U9 |
| E, Q | RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III | protein | 214 | 32% helix, 19% strand | C4R3P8 |
| F, R | RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III | protein | 84 | 31% helix, 14% strand | C4R1V1 |
| G, S | RNA polymerase II subunit | protein | 171 | 9% helix, 43% strand | C4R9A1 |
| H, T | RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III | protein | 130 | 2% helix, 42% strand | C4R273 |
| I, U | DNA-directed RNA polymerase subunit | protein | 112 | 4% helix, 23% strand | F2QPE6 |
| J, V | RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III | protein | 62 | 44% helix, 0% strand | C4R009 |
| K, W | RNA polymerase II subunit B12.5 | protein | 113 | 33% helix, 24% strand | C4R3Z5 |
| L, X | RNA polymerase subunit, found in RNA polymerase complexes I, II, and III | protein | 46 | 0% helix, 9% strand | C4QWA8 |
| M | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 1386 | 38% helix, 14% strand | C4R4Y0 |
| N | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1074 | 27% helix, 20% strand | C4QZQ7 |
| P | RNA polymerase II subunit B32 | protein | 162 | 43% helix, 7% strand | C4R2U9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, I, J, L, M, N, O, U, V, X
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 | 1190 | 0.87 | 0.88 | 136 | empty |
| 2 | 1122 | 0.87 | 0.88 | 135 | empty |
| 3 | 1047 | 0.84 | 0.85 | 100 | empty |
| 4 | 997 | 0.83 | 0.84 | 96 | empty |
| 5 | 838 | 0.81 | 0.83 | 84 | empty |
Interfaces
58 interfaces between chains.
- A–B · 9074 Ų buried · 109 hydrogen bonds · protein-protein
- M–N · 9062 Ų buried · 125 hydrogen bonds · protein-protein
- M–Q · 2118 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 2112 Ų buried · 22 hydrogen bonds · protein-protein
- D–G · 1952 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5X51 · RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) · 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 C4R4Y0
- Every structure of UniProt C4QZQ7
- Every structure of UniProt C4R7L2
- Every structure of UniProt C4R2U9
- Every structure of UniProt C4R3P8
- Every structure of UniProt C4R1V1
- Every structure of UniProt C4R9A1
- Every structure of UniProt C4R273
- Every structure of UniProt F2QPE6
- Every structure of UniProt C4R009
- Every structure of UniProt C4R3Z5
- Every structure of UniProt C4QWA8
- Elsewhere: RCSB PDB 5X51 · PDBe 5X51 · UniProt C4R4Y0 · UniProt C4QZQ7 · UniProt C4R7L2 · UniProt C4R2U9 · UniProt C4R3P8 · UniProt C4R1V1 · UniProt C4R9A1 · UniProt C4R273 · UniProt F2QPE6 · UniProt C4R009 · UniProt C4R3Z5 · UniProt C4QWA8
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