Research workbench
The X-ray crystal structure of RNA polymerase from archaea
Analyse The X-ray crystal structure of RNA polymerase from archaea in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HKZ
- Type
- protein
- Length
- 6,676 residues
- Chains
- 26
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit a'; DNA-directed RNA polymerase subunit a''…
- EC
- 2.7.7.6
- UniProt
- Q980R2, P58192, P95989, Q980A3, Q9UXD9, Q980L5, Q980Q9, Q97ZJ9, Q980K0, Q980Z8, Q97ZX7, Q980B8
- Ligands
- F3S, ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 13 distinct chains · 27% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | DNA-directed RNA polymerase subunit a' (EC 2.7.7.6) | protein | 836 | 33% helix, 9% strand | Q980R2 |
| C, M | DNA-directed RNA polymerase subunit a'' (EC 2.7.7.6) | protein | 370 | 29% helix, 9% strand | P58192 |
| B, J | DNA-directed RNA polymerase subunit B | protein | 1090 | 24% helix, 19% strand | — |
| D, O | DNA-directed RNA polymerase subunit D (EC 2.7.7.6) | protein | 264 | 25% helix, 28% strand | P95989 |
| E, Q | DNA-directed RNA polymerase, subunit E' (RPOE1) (EC 2.7.7.6) | protein | 176 | 11% helix, 35% strand | Q980A3 |
| F, R | DNA-directed RNA polymerase, subunit F (rpof) (EC 2.7.7.6) | protein | 89 | 43% helix, 9% strand | Q9UXD9 |
| G, S | DNA-directed RNA polymerase, subunit G (rpog) (EC 2.7.7.6) | protein | 113 | 0% helix, 42% strand | Q980L5 |
| H, T | DNA-directed RNA polymerase subunit H (EC 2.7.7.6) | protein | 74 | 8% helix, 14% strand | Q980Q9 |
| K, U | DNA-directed RNA polymerase subunit K (EC 2.7.7.6) | protein | 82 | 40% helix, 9% strand | Q97ZJ9 |
| L, V | DNA-directed RNA polymerase subunit L (EC 2.7.7.6) | protein | 92 | 37% helix, 27% strand | Q980K0 |
| N, W | DNA-directed RNA polymerase subunit N (EC 2.7.7.6) | protein | 64 | 47% helix, 0% strand | Q980Z8 |
| P, X | DNA-directed RNA polymerase subunit P (EC 2.7.7.6) | protein | 43 | 0% helix, 21% strand | Q97ZX7 |
| Y, Z | DNA-directed RNA polymerase subunit 13 | protein | 45 | 53% helix, 0% strand | Q980B8 |
Ligands and binding sites
- F3S · FE3-S4 cluster · ligand · 2 copies · chains D, O
- ZN · Zinc ion · metal · 10 copies · chains A, B, N, P, I, J, W, X
- MG · Magnesium ion · metal · 2 copies · chains A, I
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 | 884 | 0.85 | 0.87 | 104 | empty |
| 2 | 1068 | 0.84 | 0.85 | 98 | empty |
| 3 | 976 | 0.81 | 0.82 | 90 | empty |
| 4 | 1032 | 0.80 | 0.81 | 97 | empty |
| 5 | 869 | 0.79 | 0.82 | 73 | empty |
Interfaces
65 interfaces between chains.
- I–J · 7996 Ų buried · 117 hydrogen bonds · protein-protein
- A–B · 7964 Ų buried · 120 hydrogen bonds · protein-protein
- A–C · 4842 Ų buried · 59 hydrogen bonds · protein-protein
- I–M · 4797 Ų buried · 47 hydrogen bonds · protein-protein
- E–F · 1995 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 3HKZ · The X-ray crystal structure of RNA polymerase from Archaea · the same entry in another collection · chain N against N, 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 Q980R2
- Every structure of UniProt P58192
- Every structure of UniProt P95989
- Every structure of UniProt Q980A3
- Every structure of UniProt Q9UXD9
- Every structure of UniProt Q980L5
- Every structure of UniProt Q980Q9
- Every structure of UniProt Q97ZJ9
- Every structure of UniProt Q980K0
- Every structure of UniProt Q980Z8
- Every structure of UniProt Q97ZX7
- Every structure of UniProt Q980B8
- Elsewhere: RCSB PDB 3HKZ · PDBe 3HKZ · UniProt Q980R2 · UniProt P58192 · UniProt P95989 · UniProt Q980A3 · UniProt Q9UXD9 · UniProt Q980L5 · UniProt Q980Q9 · UniProt Q97ZJ9 · UniProt Q980K0 · UniProt Q980Z8 · UniProt Q97ZX7 · UniProt Q980B8
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