MolNFT v1 · #144651 · protein + DNA
Mtb rnap HOLO/RBPA/DOUBLE fork DNA -closed clamp
6C04 · DNA-directed RNA polymerase subunit alpha: “Mtb rnap HOLO/RBPA/DOUBLE fork DNA -closed clamp”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.81). MolNFT v1 #144651 on GenesisL1: 3D structure, binding sites…
- PDB
- 6C04
- Type
- protein + DNA
- Length
- 3,448 residues
- Chains
- 11
- Method
- electron microscopy
- 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
- A0A045J8T1, V9Z879, A0A045J9E2, A0A0T9N9K3, A0A045HD00, A0A045IP01
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 11 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 226 | 17% helix, 38% strand | A0A045J8T1 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 237 | 15% helix, 34% strand | A0A045J8T1 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 22% helix, 24% strand | V9Z879 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1267 | 42% helix, 13% strand | A0A045J9E2 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 83 | 40% helix, 5% strand | A0A0T9N9K3 |
| F | RNA polymerase sigma factor siga | protein | 319 | 62% helix, 1% strand | A0A045HD00 |
| J | RNA polymerase-binding protein rbpa | protein | 108 | 23% helix, 22% strand | A0A045IP01 |
| O | DNA (31-mer) | dna | 31 | — | — |
| P | DNA (26-mer) | dna | 26 | — | — |
| G | DNA (26-mer) | dna | 18 | — | — |
| H | DNA (31-mer) | dna | 22 | — | — |
Ligands and binding sites
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 | 500 | 0.81 | 0.88 | 62 | empty |
| 2 | 834 | 0.81 | 0.84 | 69 | empty |
| 3 | 776 | 0.80 | 0.83 | 74 | empty |
| 4 | 853 | 0.78 | 0.81 | 84 | empty |
| 5 | 1118 | 0.76 | 0.79 | 103 | empty |
Interfaces
24 interfaces between chains.
- C–D · 8353 Ų buried · 84 hydrogen bonds · protein-protein
- D–F · 2505 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2501 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 2187 Ų buried · 23 hydrogen bonds · protein-protein
- C–F · 2092 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6C04 · Mtb RNAP Holo/RbpA/double fork DNA -closed clamp · the same entry in another collection · chain H against H, 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 A0A045J8T1
- Every structure of UniProt V9Z879
- Every structure of UniProt A0A045J9E2
- Every structure of UniProt A0A0T9N9K3
- Every structure of UniProt A0A045HD00
- Every structure of UniProt A0A045IP01
- Elsewhere: RCSB PDB 6C04 · PDBe 6C04 · UniProt A0A045J8T1 · UniProt V9Z879 · UniProt A0A045J9E2 · UniProt A0A0T9N9K3 · UniProt A0A045HD00 · UniProt A0A045IP01
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