Research workbench
Crystal structure of human carboxy-terminal domain RNA polymerase II polypeptide a small phosphatase 2
Analyse Crystal structure of human carboxy-terminal domain RNA polymerase II… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q5E
- Type
- protein
- Length
- 1,427 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxy-terminal domain RNA polymerase II polypeptide a small phosphatase 2
- EC
- 3.1.3.16
- UniProt
- O14595
- Ligands
- MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxy-terminal domain RNA polymerase II polypeptide a small phosphatase 2 (EC 3.1.3.16) | protein | 181 | 32% helix, 27% strand | O14595 |
| B, C | Carboxy-terminal domain RNA polymerase II polypeptide a small phosphatase 2 (EC 3.1.3.16) | protein | 178 | 31% helix, 28% strand | O14595 |
| D | Carboxy-terminal domain RNA polymerase II polypeptide a small phosphatase 2 (EC 3.1.3.16) | protein | 175 | 30% helix, 26% strand | O14595 |
| E | Carboxy-terminal domain RNA polymerase II polypeptide a small phosphatase 2 (EC 3.1.3.16) | protein | 179 | 31% helix, 26% strand | O14595 |
| F | Carboxy-terminal domain RNA polymerase II polypeptide a small phosphatase 2 (EC 3.1.3.16) | protein | 178 | 34% helix, 26% strand | O14595 |
| G, H | Carboxy-terminal domain RNA polymerase II polypeptide a small phosphatase 2 (EC 3.1.3.16) | protein | 179 | 31% helix, 26% strand | O14595 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.82 | 0.87 | 73 | MG |
| 2 | 569 | 0.82 | 0.88 | 65 | MG |
| 3 | 743 | 0.81 | 0.85 | 65 | MG |
| 4 | 686 | 0.80 | 0.85 | 58 | MG |
| 5 | 997 | 0.70 | 0.74 | 87 | empty |
Interfaces
16 interfaces between chains.
- A–F · 561 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 558 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 550 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 502 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 498 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2Q5E · Crystal structure of human carboxy-terminal domain RNA polymerase II polypeptide A small… · the same entry in another collection · chain H against H, TM-score 1.00
- O14595 · AlphaFold monomer V2.0 prediction for carboxy-terminal domain RNA polymerase II… · a predicted model of the same protein · chain D against A, TM-score 0.99
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 O14595
- Elsewhere: RCSB PDB 2Q5E · PDBe 2Q5E · UniProt O14595
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