Research workbench
Cryo-EM structure of the sulfolobus acidocaldarius RNA polymerase at 2.88 a
Analyse Cryo-EM structure of the sulfolobus acidocaldarius RNA polymerase at 2.88 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OK0
- Type
- protein
- Length
- 3,234 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit a'; DNA-directed RNA polymerase subunit B…
- EC
- 2.7.7.6
- UniProt
- P11512, P11513, P11514, P39471, P39466, Q4JB12, Q4JAY4, P11521, P39463, P46217, P39472, Q4JAE8, Q4JAJ6
- Ligands
- F3S, ZN, MG
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 13 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit a' (EC 2.7.7.6) | protein | 880 | 39% helix, 17% strand | P11512 |
| B | DNA-directed RNA polymerase subunit B (EC 2.7.7.6) | protein | 1109 | 31% helix, 25% strand | P11513 |
| C | DNA-directed RNA polymerase subunit a'' (EC 2.7.7.6) | protein | 393 | 46% helix, 12% strand | P11514 |
| D | DNA-directed RNA polymerase subunit D (EC 2.7.7.6) | protein | 261 | 24% helix, 34% strand | P39471 |
| E | DNA-directed RNA polymerase subunit E (EC 2.7.7.6) | protein | 51 | 29% helix, 33% strand | P39466 |
| F | DNA-directed RNA polymerase, subunit F (EC 2.7.7.6) | protein | 7 | 0% helix, 14% strand | Q4JB12 |
| G | DNA-directed RNA polymerase, subunit G (EC 2.7.7.6) | protein | 122 | 5% helix, 54% strand | Q4JAY4 |
| H | DNA-directed RNA polymerase subunit H (EC 2.7.7.6) | protein | 78 | 24% helix, 32% strand | P11521 |
| K | DNA-directed RNA polymerase subunit K (EC 2.7.7.6) | protein | 86 | 42% helix, 13% strand | P39463 |
| L | DNA-directed RNA polymerase subunit L (EC 2.7.7.6) | protein | 90 | 38% helix, 32% strand | P46217 |
| N | DNA-directed RNA polymerase subunit N (EC 2.7.7.6) | protein | 66 | 48% helix, 3% strand | P39472 |
| P | DNA-directed RNA polymerase subunit P (EC 2.7.7.6) | protein | 47 | 0% helix, 30% strand | Q4JAE8 |
| Q | Conserved protein | protein | 44 | 80% helix, 0% strand | Q4JAJ6 |
Ligands and binding sites
- F3S · FE3-S4 cluster · ligand · chains D
- ZN · Zinc ion · metal · 6 copies · chains A, B, N, P
- MG · Magnesium ion · metal · chains A
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 | 769 | 0.78 | 0.82 | 80 | empty |
| 2 | 920 | 0.77 | 0.80 | 98 | empty |
| 3 | 1009 | 0.77 | 0.79 | 84 | empty |
| 4 | 493 | 0.74 | 0.83 | 53 | empty |
| 5 | 985 | 0.73 | 0.77 | 96 | empty |
Interfaces
28 interfaces between chains.
- A–B · 8207 Ų buried · 87 hydrogen bonds · protein-protein
- A–C · 5029 Ų buried · 39 hydrogen bonds · protein-protein
- B–N · 1772 Ų buried · 15 hydrogen bonds · protein-protein
- D–L · 1751 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1598 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7OK0 · Cryo-EM structure of the Sulfolobus acidocaldarius RNA polymerase at 2.88 A · the same entry in another collection · chain Q against Q, 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 P11512
- Every structure of UniProt P11513
- Every structure of UniProt P11514
- Every structure of UniProt P39471
- Every structure of UniProt P39466
- Every structure of UniProt Q4JB12
- Every structure of UniProt Q4JAY4
- Every structure of UniProt P11521
- Every structure of UniProt P39463
- Every structure of UniProt P46217
- Every structure of UniProt P39472
- Every structure of UniProt Q4JAE8
- Every structure of UniProt Q4JAJ6
- Elsewhere: RCSB PDB 7OK0 · PDBe 7OK0 · UniProt P11512 · UniProt P11513 · UniProt P11514 · UniProt P39471 · UniProt P39466 · UniProt Q4JB12 · UniProt Q4JAY4 · UniProt P11521 · UniProt P39463 · UniProt P46217 · UniProt P39472 · UniProt Q4JAE8 · UniProt Q4JAJ6
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