Research workbench
E. COLI transcription initiation complex - 16-bp spacer and 4-nt RNA
Analyse E. COLI transcription initiation complex - 16-bp spacer and 4-nt RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YLO
- Type
- protein + DNA + RNA
- Length
- 11,550 residues
- Chains
- 27
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- A7ZSI4, A7ZUK1, A7ZUK2, A7ZTK1, P00579
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 9 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, M | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 24% helix, 39% strand | A7ZSI4 |
| B, H, N | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 24% helix, 39% strand | A7ZSI4 |
| C, I, O | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1341 | 32% helix, 23% strand | A7ZUK1 |
| D, J, P | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1362 | 38% helix, 16% strand | A7ZUK2 |
| E, K, Q | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 90 | 73% helix, 0% strand | A7ZTK1 |
| F, L, R | RNA polymerase sigma factor rpod | protein | 497 | 69% helix, 1% strand | P00579 |
| 1, 4, 7 | Nt strand DNA (49-mer) | dna | 49 | — | — |
| 2, 5, 8 | T strand DNA (49-mer) | dna | 49 | — | — |
| 3, 6, 9 | RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3') | rna | 4 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains D, J, P
- MG · Magnesium ion · metal · 3 copies · chains C, D, J, 6, P, 9
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 | 1173 | 0.86 | 0.87 | 137 | empty |
| 2 | 1189 | 0.85 | 0.87 | 113 | empty |
| 3 | 935 | 0.85 | 0.86 | 99 | empty |
| 4 | 807 | 0.85 | 0.88 | 95 | empty |
| 5 | 994 | 0.85 | 0.86 | 96 | empty |
Interfaces
67 interfaces between chains.
- I–J · 9093 Ų buried · 114 hydrogen bonds · protein-protein
- O–P · 9056 Ų buried · 88 hydrogen bonds · protein-protein
- C–D · 8880 Ų buried · 100 hydrogen bonds · protein-protein
- P–R · 3258 Ų buried · 34 hydrogen bonds · protein-protein
- D–F · 3105 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 modified (disulfide, nucleotide modification).
Compared structures
- 4YLO · E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA · the same entry in another collection · chain B against B, 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 A7ZSI4
- Every structure of UniProt A7ZUK1
- Every structure of UniProt A7ZUK2
- Every structure of UniProt A7ZTK1
- Every structure of UniProt P00579
- Elsewhere: RCSB PDB 4YLO · PDBe 4YLO · UniProt A7ZSI4 · UniProt A7ZUK1 · UniProt A7ZUK2 · UniProt A7ZTK1 · UniProt P00579
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