MolNFT v1 · #184377 · protein + DNA + RNA
Pol II-csb-csa-DDB1-uvssa-ADPBEF3 (STRUCTURE2)
7OOB · DNA-directed RNA polymerase II subunit RPB1: “Pol II-csb-csa-DDB1-uvssa-ADPBEF3 (STRUCTURE2)”. Electron microscopy, 4 ligands (ADP, BEF, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #184377 on GenesisL1: 3D structure, binding…
- PDB
- 7OOB
- Type
- protein + DNA + RNA
- Length
- 5,642 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase II subunit RPB1; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6, 3.6.4.-
- UniProt
- P11414, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, F1SKN8, I3LJZ9, A0A4X1ULF2, P60899, A0A4X1VYD0, A0A4X1UK25, I3LN51, Q03468, Q16531, Q13216
- Ligands
- ADP, BEF, ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 18 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 | protein | 1412 | 42% helix, 16% strand | P11414 |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1131 | 29% helix, 25% strand | I3LGP4 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 260 | 25% helix, 28% strand | I3LCH3 |
| D | RPOL4C domain-containing protein | protein | 126 | 58% helix, 3% strand | A0A287ADR4 |
| E | DNA-directed RNA polymerase II subunit E | protein | 209 | 42% helix, 25% strand | I3LSI7 |
| F | DNA-directed RNA polymerase II subunit F | protein | 82 | 33% helix, 16% strand | F1SKN8 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 9% helix, 51% strand | I3LJZ9 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 148 | 5% helix, 49% strand | A0A4X1ULF2 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 117 | 4% helix, 30% strand | P60899 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 67 | 42% helix, 4% strand | A0A4X1VYD0 |
| K | RNA_POL_L_2 domain-containing protein | protein | 115 | 42% helix, 23% strand | A0A4X1UK25 |
| L | RNA polymerase II subunit K | protein | 46 | 0% helix, 26% strand | I3LN51 |
| b | DNA excision repair protein ercc-6 (EC 3.6.4.-) | protein | 520 | 48% helix, 12% strand | Q03468 |
| d | DNA damage-binding protein 1 | protein | 781 | 8% helix, 51% strand | Q16531 |
| N | Nts | dna | 35 | — | — |
| T | Ts | dna | 47 | — | — |
| P | RNA | rna | 10 | — | — |
| a | DNA excision repair protein ercc-8 | protein | 365 | 6% helix, 43% strand | Q13216 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains b
- BEF · Beryllium trifluoride ion · ligand · chains b
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
- MG · Magnesium ion · metal · 2 copies · chains A, P, b
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 | 694 | 0.87 | 0.92 | 88 | empty |
| 2 | 1095 | 0.85 | 0.86 | 138 | empty |
| 3 | 388 | 0.85 | 0.94 | 45 | empty |
| 4 | 567 | 0.83 | 0.88 | 68 | empty |
| 5 | 442 | 0.83 | 0.90 | 47 | empty |
Interfaces
41 interfaces between chains.
- A–B · 9099 Ų buried · 128 hydrogen bonds · protein-protein
- d–a · 2552 Ų buried · 36 hydrogen bonds · protein-protein
- A–E · 2415 Ų buried · 29 hydrogen bonds · protein-protein
- C–K · 2281 Ų buried · 21 hydrogen bonds · protein-protein
- A–H · 2159 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 7OOB · Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2) · the same entry in another collection · chain a against a, 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 P11414
- Every structure of UniProt I3LGP4
- Every structure of UniProt I3LCH3
- Every structure of UniProt A0A287ADR4
- Every structure of UniProt I3LSI7
- Every structure of UniProt F1SKN8
- Every structure of UniProt I3LJZ9
- Every structure of UniProt A0A4X1ULF2
- Every structure of UniProt P60899
- Every structure of UniProt A0A4X1VYD0
- Every structure of UniProt A0A4X1UK25
- Every structure of UniProt I3LN51
- Every structure of UniProt Q03468
- Every structure of UniProt Q16531
- Every structure of UniProt Q13216
- Elsewhere: RCSB PDB 7OOB · PDBe 7OOB · UniProt P11414 · UniProt I3LGP4 · UniProt I3LCH3 · UniProt A0A287ADR4 · UniProt I3LSI7 · UniProt F1SKN8 · UniProt I3LJZ9 · UniProt A0A4X1ULF2 · UniProt P60899 · UniProt A0A4X1VYD0 · UniProt A0A4X1UK25 · UniProt I3LN51 · UniProt Q03468 · UniProt Q16531 · UniProt Q13216
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