Research workbench
Crystal structure of sulfolobus shibatae RNA polymerase in P21 space group
Analyse Crystal structure of sulfolobus shibatae RNA polymerase in P21 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y0S
- Type
- protein
- Length
- 6,610 residues
- Chains
- 26
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase; DNA-directed RNA polymerase subunit a''; DNA-directed RNA…
- EC
- 2.7.7.6
- UniProt
- B8YB53, B8YB55, B8YB54, B8YB56, B8YB57, B8YB58, B8YB59, B8YB60, B8YB61, B8YB65, B8YB62, B8YB63, B8YB64
- Ligands
- F3S, ZN, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 13 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, W | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 831 | 36% helix, 14% strand | B8YB53 |
| B, R | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 1085 | 27% helix, 20% strand | B8YB55 |
| C, Y | DNA-directed RNA polymerase subunit a'' (EC 2.7.7.6) | protein | 368 | 40% helix, 10% strand | B8YB54 |
| D, S | DNA-directed RNA polymerase subunit D (EC 2.7.7.6) | protein | 262 | 24% helix, 31% strand | B8YB56 |
| E, T | RNA polymerase subunit 4 (EC 2.7.7.6) | protein | 164 | 8% helix, 42% strand | B8YB57 |
| F, U | RNA polymerase subunit 7 | protein | 90 | 42% helix, 3% strand | B8YB58 |
| G, V | RNA polymerase subunit 8 | protein | 110 | 0% helix, 47% strand | B8YB59 |
| H, Z | DNA-directed RNA polymerase subunit H (EC 2.7.7.6) | protein | 74 | 26% helix, 23% strand | B8YB60 |
| I, K | DNA-directed RNA polymerase subunit K (EC 2.7.7.6) | protein | 82 | 41% helix, 11% strand | B8YB61 |
| J, Q | RNA polymerase subunit 13 | protein | 39 | 54% helix, 0% strand | B8YB65 |
| L, M | DNA-directed RNA polymerase subunit L (EC 2.7.7.6) | protein | 91 | 36% helix, 29% strand | B8YB62 |
| N, O | DNA-directed RNA polymerase subunit N (EC 2.7.7.6) | protein | 64 | 47% helix, 0% strand | B8YB63 |
| P, X | RNA polymerase subunit 12 | protein | 45 | 0% helix, 11% strand | B8YB64 |
Ligands and binding sites
- F3S · FE3-S4 cluster · ligand · 2 copies · chains D, S
- ZN · Zinc ion · metal · 14 copies · chains A, B, N, O, P, R, W, X
- MG · Magnesium ion · metal · 2 copies · chains A, W
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 | 1065 | 0.78 | 0.80 | 82 | empty |
| 2 | 1048 | 0.78 | 0.80 | 87 | empty |
| 3 | 895 | 0.77 | 0.80 | 98 | empty |
| 4 | 876 | 0.77 | 0.80 | 85 | empty |
| 5 | 1007 | 0.75 | 0.78 | 78 | empty |
Interfaces
64 interfaces between chains.
- R–W · 8267 Ų buried · 109 hydrogen bonds · protein-protein
- A–B · 8249 Ų buried · 109 hydrogen bonds · protein-protein
- W–Y · 4800 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 4781 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 1850 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide (disulfide).
Compared structures
- 2Y0S · Crystal structure of Sulfolobus shibatae RNA polymerase in P21 space group · 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 B8YB53
- Every structure of UniProt B8YB55
- Every structure of UniProt B8YB54
- Every structure of UniProt B8YB56
- Every structure of UniProt B8YB57
- Every structure of UniProt B8YB58
- Every structure of UniProt B8YB59
- Every structure of UniProt B8YB60
- Every structure of UniProt B8YB61
- Every structure of UniProt B8YB65
- Every structure of UniProt B8YB62
- Every structure of UniProt B8YB63
- Every structure of UniProt B8YB64
- Elsewhere: RCSB PDB 2Y0S · PDBe 2Y0S · UniProt B8YB53 · UniProt B8YB55 · UniProt B8YB54 · UniProt B8YB56 · UniProt B8YB57 · UniProt B8YB58 · UniProt B8YB59 · UniProt B8YB60 · UniProt B8YB61 · UniProt B8YB65 · UniProt B8YB62 · UniProt B8YB63 · UniProt B8YB64
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