Research workbench
Cryo-EM structure of xanthomonos oryzae transcription elongation complex with the bacteriophage protein P7
Analyse Cryo-EM structure of xanthomonos oryzae transcription elongation complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J9F
- Type
- protein + DNA + RNA
- Length
- 3,122 residues
- Chains
- 9
- 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
- B2SQT4, Q2NZX8, B2SQQ2, A0A0U4VN94, Q8LTJ5
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 9 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 215 | 22% helix, 35% strand | B2SQT4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 203 | 21% helix, 34% strand | B2SQT4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1296 | 28% helix, 21% strand | Q2NZX8 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1215 | 37% helix, 14% strand | B2SQQ2 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 64 | 66% helix, 0% strand | A0A0U4VN94 |
| G | DNA (29-mer) | dna | 29 | — | — |
| H | DNA (29-mer) | dna | 22 | — | — |
| I | RNA (5'-R(P*AP*GP*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3') | rna | 12 | — | — |
| J | 45L | protein | 66 | 27% helix, 32% strand | Q8LTJ5 |
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 | 961 | 0.85 | 0.87 | 104 | empty |
| 2 | 965 | 0.83 | 0.84 | 98 | empty |
| 3 | 994 | 0.81 | 0.82 | 79 | empty |
| 4 | 967 | 0.80 | 0.82 | 80 | empty |
| 5 | 117 | 0.79 | 0.96 | 29 | empty |
Interfaces
17 interfaces between chains.
- C–D · 8183 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 1644 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1453 Ų buried · 6 hydrogen bonds · protein-protein
- D–G · 1063 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–E · 956 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6J9F · Cryo-EM structure of Xanthomonos oryzae transcription elongation complex with the… · the same entry in another collection · chain J against J, TM-score 1.00
- Q2NZX8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q2NZX8) · a predicted model of the same protein · chain C against A, TM-score 0.98
- B2SQQ2 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (B2SQQ2) · a predicted model of the same protein · chain D against A, TM-score 0.95
- B2SQT4 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (B2SQT4) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 B2SQT4
- Every structure of UniProt Q2NZX8
- Every structure of UniProt B2SQQ2
- Every structure of UniProt A0A0U4VN94
- Every structure of UniProt Q8LTJ5
- Elsewhere: RCSB PDB 6J9F · PDBe 6J9F · UniProt B2SQT4 · UniProt Q2NZX8 · UniProt B2SQQ2 · UniProt A0A0U4VN94 · UniProt Q8LTJ5
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