MolNFT v1 · #156503 · protein + DNA
Cryo-EM structure of thermus thermophilus mfd in complex with RNA polymerase and ATP-gamma-S
6M6B · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of thermus thermophilus mfd in complex with RNA polymerase and ATP-gamma-S”. Electron microscopy, 3 ligands (AGS, ZN, MG), 20 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 6M6B
- Type
- protein + DNA
- Length
- 3,473 residues
- Chains
- 8
- 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, 3.6.4.-
- UniProt
- Q5SHR6, Q8RQE9, Q8RQE8, Q8RQE7, Q72KB4
- Ligands
- AGS, ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 8 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 226 | 22% helix, 39% strand | Q5SHR6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 21% helix, 42% strand | Q5SHR6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 28% helix, 26% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1305 | 40% helix, 18% strand | Q8RQE8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 49% helix, 10% strand | Q8RQE7 |
| M | Transcription-repair-coupling factor (EC 3.6.4.-) | protein | 459 | 40% helix, 17% strand | Q72KB4 |
| T | Template strand DNA | dna | 28 | — | — |
| N | Nontemplate strand DNA | dna | 28 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · chains M
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · chains D
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 | 1089 | 0.86 | 0.87 | 122 | empty |
| 2 | 227 | 0.83 | 0.94 | 48 | empty |
| 3 | 301 | 0.82 | 0.93 | 36 | empty |
| 4 | 358 | 0.76 | 0.87 | 57 | empty |
| 5 | 740 | 0.76 | 0.81 | 79 | empty |
Interfaces
18 interfaces between chains.
- C–D · 8575 Ų buried · 96 hydrogen bonds · protein-protein
- D–E · 2371 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2069 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1452 Ų buried · 6 hydrogen bonds · protein-protein
- T–N · 1343 Ų buried · 151 hydrogen bonds · nucleic-nucleic
Compared structures
- 6M6B · Cryo-EM structure of Thermus thermophilus Mfd in complex with RNA polymerase and… · the same entry in another collection · chain N against N, TM-score 1.00
- Q8RQE7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q8RQE7) · a predicted model of the same protein · chain E against A, TM-score 0.96
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 Q5SHR6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q8RQE7
- Every structure of UniProt Q72KB4
- Elsewhere: RCSB PDB 6M6B · PDBe 6M6B · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q72KB4
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