MolNFT v1 · #182215 · protein + DNA + RNA
Complex structure of trailing ec of EC+EC (trailing ec-focused)
7MK9 · DNA (40-mer): “Complex structure of trailing ec of EC+EC (trailing ec-focused)”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.88). MolNFT v1 #182215 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7MK9
- Type
- protein + DNA + RNA
- Length
- 4,414 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (40-mer); DNA-directed RNA polymerase subunit; DNA-directed RNA polymerase subunit…
- EC
- 2.7.7.6
- UniProt
- A0A6A5Q1P2, A0A6A5Q4H2, A0A6A5Q0Z3, A0A6A5PTI6, A0A6A5Q456, A0A6L0ZRI7, A0A6A5Q270, A0A6A5Q8C2, A0A7I9EWC2, A0A6A5Q7Q6, A0A6A5Q7A1, A0A6A5PY05, P41895, A0A6A5PZ00
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 17 distinct chains · 30% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | DNA (40-mer) | dna | 40 | — | — |
| O | DNA (40-mer) | dna | 40 | — | — |
| A | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 1425 | 39% helix, 14% strand | A0A6A5Q1P2 |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1166 | 27% helix, 20% strand | A0A6A5Q4H2 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 265 | 21% helix, 26% strand | A0A6A5Q0Z3 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 168 | 60% helix, 5% strand | A0A6A5PTI6 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 38% helix, 20% strand | A0A6A5Q456 |
| F | DNA-directed RNA polymerases I,II,AND III subunit RPABC2 | protein | 87 | 31% helix, 15% strand | A0A6L0ZRI7 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 7% helix, 43% strand | A0A6A5Q270 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 135 | 0% helix, 45% strand | A0A6A5Q8C2 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 114 | 3% helix, 27% strand | A0A7I9EWC2 |
| J | DNA-directed RNA polymerases II subunit RPABC5 | protein | 66 | 42% helix, 2% strand | A0A6A5Q7Q6 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 115 | 39% helix, 24% strand | A0A6A5Q7A1 |
| L | DNA-directed RNA polymerases II subunit RPABC4 | protein | 44 | 0% helix, 11% strand | A0A6A5PY05 |
| R | RNA (5'-R(P*UP*CP*GP*AP*GP*AP*GP*GP*AP*UP*CP*CP*CP*AP*A)- 3') | rna | 15 | — | — |
| Q | Transcription initiation factor iif subunit alpha | protein | 214 | 31% helix, 21% strand | P41895 |
| M | Transcription initiation factor iif subunit beta | protein | 135 | 16% helix, 39% strand | A0A6A5PZ00 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, D, C, I, J, L
- MG · Magnesium ion · metal · 2 copies · chains A, R
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 | 1135 | 0.88 | 0.89 | 125 | empty |
| 2 | 794 | 0.87 | 0.90 | 86 | empty |
| 3 | 1067 | 0.86 | 0.87 | 111 | empty |
| 4 | 807 | 0.85 | 0.88 | 88 | empty |
| 5 | 750 | 0.84 | 0.88 | 90 | empty |
Interfaces
41 interfaces between chains.
- A–B · 9061 Ų buried · 95 hydrogen bonds · protein-protein
- Q–M · 3157 Ų buried · 67 hydrogen bonds · protein-protein
- B–Q · 2336 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 2116 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 2082 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7MK9 · Complex structure of trailing EC of EC+EC (trailing EC-focused) · the same entry in another collection · chain M against M, 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 A0A6A5Q1P2
- Every structure of UniProt A0A6A5Q4H2
- Every structure of UniProt A0A6A5Q0Z3
- Every structure of UniProt A0A6A5PTI6
- Every structure of UniProt A0A6A5Q456
- Every structure of UniProt A0A6L0ZRI7
- Every structure of UniProt A0A6A5Q270
- Every structure of UniProt A0A6A5Q8C2
- Every structure of UniProt A0A7I9EWC2
- Every structure of UniProt A0A6A5Q7Q6
- Every structure of UniProt A0A6A5Q7A1
- Every structure of UniProt A0A6A5PY05
- Every structure of UniProt P41895
- Every structure of UniProt A0A6A5PZ00
- Elsewhere: RCSB PDB 7MK9 · PDBe 7MK9 · UniProt A0A6A5Q1P2 · UniProt A0A6A5Q4H2 · UniProt A0A6A5Q0Z3 · UniProt A0A6A5PTI6 · UniProt A0A6A5Q456 · UniProt A0A6L0ZRI7 · UniProt A0A6A5Q270 · UniProt A0A6A5Q8C2 · UniProt A0A7I9EWC2 · UniProt A0A6A5Q7Q6 · UniProt A0A6A5Q7A1 · UniProt A0A6A5PY05 · UniProt P41895 · UniProt A0A6A5PZ00
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