MolNFT v1 · #137230 · protein + DNA
Structure of a mycobacterium smegmatis transcription initiation complex with an upstream-fork promoter fragment
5VI8: “Structure of a mycobacterium smegmatis transcription initiation complex with an upstream-fork promoter…”. X-ray diffraction, 3 ligands (ZN, MG, SO4). MolNFT v1 #137230 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VI8
- Type
- protein + DNA
- Length
- 3,386 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- A0QZ11, A0QSL8, P60281, A0QS66, A0QWT1, A0QW02
- Ligands
- ZN, MG, SO4
Structure
x-ray diffraction · 10 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J | — | protein | 83 | — | A0QZ11 |
| A | — | protein | 218 | — | A0QSL8 |
| B | — | protein | 233 | — | A0QSL8 |
| C | — | protein | 1099 | — | P60281 |
| D | — | protein | 1248 | — | A0QS66 |
| E | — | protein | 76 | — | A0QWT1 |
| F | — | protein | 319 | — | A0QW02 |
| O | — | dna | 31 | — | — |
| P | — | dna | 26 | — | — |
| T | — | protein | 53 | — | A0QSL8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · chains D
- SO4 · Sulfate ion · ion · 12 copies · chains C, D, F
- EDO · 1,2-ethanediol · additive · 6 copies · chains C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5VI8 · Structure of a mycobacterium smegmatis transcription initiation complex with an… · the same entry in another collection · chain T against T, TM-score 1.00
- P60281 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P60281) · a predicted model of the same protein · chain C against A, TM-score 0.99
- A0QS66 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (A0QS66) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 A0QZ11
- Every structure of UniProt A0QSL8
- Every structure of UniProt P60281
- Every structure of UniProt A0QS66
- Every structure of UniProt A0QWT1
- Every structure of UniProt A0QW02
- Elsewhere: RCSB PDB 5VI8 · PDBe 5VI8 · UniProt A0QZ11 · UniProt A0QSL8 · UniProt P60281 · UniProt A0QS66 · UniProt A0QWT1 · UniProt A0QW02
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