MolNFT v1 · #182216 · protein + DNA + RNA
Structure of EC+EC (leading ec-focused)
7MKA · DNA (40-mer): “Structure of EC+EC (leading ec-focused)”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.88). MolNFT v1 #182216 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7MKA
- Type
- protein + DNA + RNA
- Length
- 4,059 residues
- Chains
- 15
- 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
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 15 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | DNA (40-mer) | dna | 39 | — | — |
| O | DNA (40-mer) | dna | 40 | — | — |
| a | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 1425 | 38% helix, 13% strand | A0A6A5Q1P2 |
| b | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1160 | 28% helix, 21% strand | A0A6A5Q4H2 |
| c | DNA-directed RNA polymerase II subunit RPB3 | protein | 265 | 24% helix, 23% strand | A0A6A5Q0Z3 |
| d | DNA-directed RNA polymerase II subunit RPB4 | protein | 168 | 59% helix, 3% strand | A0A6A5PTI6 |
| e | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 35% helix, 19% 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 | 9% helix, 37% strand | A0A6A5Q270 |
| h | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 135 | 0% helix, 44% strand | A0A6A5Q8C2 |
| i | DNA-directed RNA polymerase II subunit RPB9 | protein | 114 | 3% helix, 26% strand | A0A7I9EWC2 |
| j | DNA-directed RNA polymerases II subunit RPABC5 | protein | 66 | 47% helix, 0% strand | A0A6A5Q7Q6 |
| k | DNA-directed RNA polymerase II subunit RPB11 | protein | 115 | 38% helix, 24% strand | A0A6A5Q7A1 |
| l | DNA-directed RNA polymerases II subunit RPABC4 | protein | 44 | 0% helix, 9% strand | A0A6A5PY05 |
| r | RNA (5'- R(P*AP*AP*CP*UP*AP*GP*UP*UP*AP*AP*GP*AP*GP*GP*UP*U)-3') | rna | 16 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains a, b, 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 | 1107 | 0.88 | 0.89 | 134 | empty |
| 2 | 1136 | 0.84 | 0.85 | 94 | empty |
| 3 | 479 | 0.84 | 0.91 | 59 | empty |
| 4 | 881 | 0.83 | 0.85 | 101 | empty |
| 5 | 772 | 0.82 | 0.85 | 85 | empty |
Interfaces
37 interfaces between chains.
- a–b · 8886 Ų buried · 84 hydrogen bonds · protein-protein
- a–e · 2093 Ų buried · 20 hydrogen bonds · protein-protein
- a–f · 2045 Ų buried · 16 hydrogen bonds · protein-protein
- c–k · 1997 Ų buried · 7 hydrogen bonds · protein-protein
- d–g · 1939 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7MKA · Structure of EC+EC (leading EC-focused) · the same entry in another collection · chain N against N, 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
- Elsewhere: RCSB PDB 7MKA · PDBe 7MKA · UniProt A0A6A5Q1P2 · UniProt A0A6A5Q4H2 · UniProt A0A6A5Q0Z3 · UniProt A0A6A5PTI6 · UniProt A0A6A5Q456 · UniProt A0A6L0ZRI7 · UniProt A0A6A5Q270 · UniProt A0A6A5Q8C2 · UniProt A0A7I9EWC2 · UniProt A0A6A5Q7Q6 · UniProt A0A6A5Q7A1 · UniProt A0A6A5PY05
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