Research workbench
Pol II-csb-csa-DDB1-uvssa (STRUCTURE1)
Analyse Pol II-csb-csa-DDB1-uvssa (STRUCTURE1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OO3
- Type
- protein + DNA + RNA
- Length
- 6,147 residues
- Chains
- 20
- 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, Q13216, Q03468, Q2YD98, Q16531
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 20 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 |
| N | Nts | dna | 35 | — | — |
| T | Ts | dna | 47 | — | — |
| P | RNA | rna | 10 | — | — |
| a | DNA excision repair protein ercc-8 | protein | 365 | 6% helix, 42% strand | Q13216 |
| b | DNA excision repair protein ercc-6 (EC 3.6.4.-) | protein | 534 | 48% helix, 11% strand | Q03468 |
| x | Csb element | protein | 35 | 49% helix, 11% strand | — |
| c | UV-stimulated scaffold protein a | protein | 141 | 69% helix, 0% strand | Q2YD98 |
| d | DNA damage-binding protein 1 | protein | 1096 | 6% helix, 50% strand | Q16531 |
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 | 1015 | 0.88 | 0.90 | 113 | empty |
| 2 | 1073 | 0.87 | 0.88 | 122 | empty |
| 3 | 1054 | 0.86 | 0.87 | 133 | empty |
| 4 | 883 | 0.86 | 0.88 | 108 | empty |
| 5 | 933 | 0.83 | 0.84 | 89 | empty |
Interfaces
44 interfaces between chains.
- A–B · 9091 Ų buried · 128 hydrogen bonds · protein-protein
- a–d · 2509 Ų buried · 36 hydrogen bonds · protein-protein
- A–E · 2410 Ų buried · 29 hydrogen bonds · protein-protein
- C–K · 2287 Ų buried · 21 hydrogen bonds · protein-protein
- A–H · 2166 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 7OO3 · Pol II-CSB-CSA-DDB1-UVSSA (Structure1) · the same entry in another collection · chain L against L, 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 Q13216
- Every structure of UniProt Q03468
- Every structure of UniProt Q2YD98
- Every structure of UniProt Q16531
- Elsewhere: RCSB PDB 7OO3 · PDBe 7OO3 · 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 Q13216 · UniProt Q03468 · UniProt Q2YD98 · UniProt Q16531
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