Research workbench
Rnap at 3.2ANG
Analyse Rnap at 3.2ANG in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AYB
- Type
- protein
- Length
- 3,412 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase
- EC
- 2.7.7.6
- UniProt
- B8YB53, B8YB55, B8YB54, B8YB56, B8YB57, B8YB58, B8YB59, B8YB60, B8YB61, B8YB62, B8YB63, B8YB64, B8YB65
- Ligands
- SF4, ZN, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 13 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 872 | 38% helix, 16% strand | B8YB53 |
| B | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 1103 | 30% helix, 24% strand | B8YB55 |
| C | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 376 | 48% helix, 14% strand | B8YB54 |
| D | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 262 | 24% helix, 32% strand | B8YB56 |
| E | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 171 | 13% helix, 48% strand | B8YB57 |
| F | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 105 | 39% helix, 8% strand | B8YB58 |
| G | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 113 | 5% helix, 47% strand | B8YB59 |
| H | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 76 | 26% helix, 32% strand | B8YB60 |
| K | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 84 | 42% helix, 12% strand | B8YB61 |
| L | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 91 | 38% helix, 26% strand | B8YB62 |
| N | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 65 | 40% helix, 3% strand | B8YB63 |
| P | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 44 | 0% helix, 14% strand | B8YB64 |
| Q | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 50 | 80% helix, 0% strand | B8YB65 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains D
- ZN · Zinc ion · metal · 10 copies · chains A, C, 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 | 120 | 0.78 | 0.96 | 25 | empty |
| 2 | 1002 | 0.78 | 0.80 | 77 | empty |
| 3 | 1190 | 0.77 | 0.79 | 120 | empty |
| 4 | 1026 | 0.77 | 0.79 | 83 | empty |
| 5 | 1017 | 0.76 | 0.79 | 121 | empty |
Interfaces
29 interfaces between chains.
- A–B · 8409 Ų buried · 124 hydrogen bonds · protein-protein
- A–C · 4749 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 1808 Ų buried · 20 hydrogen bonds · protein-protein
- B–N · 1670 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1636 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 4AYB · RNAP at 3.2Ang · 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 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 B8YB62
- Every structure of UniProt B8YB63
- Every structure of UniProt B8YB64
- Every structure of UniProt B8YB65
- Elsewhere: RCSB PDB 4AYB · PDBe 4AYB · UniProt B8YB53 · UniProt B8YB55 · UniProt B8YB54 · UniProt B8YB56 · UniProt B8YB57 · UniProt B8YB58 · UniProt B8YB59 · UniProt B8YB60 · UniProt B8YB61 · UniProt B8YB62 · UniProt B8YB63 · UniProt B8YB64 · UniProt B8YB65
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