MolNFT v1 · #168640 · protein
Crystal structure of human rev-erbbeta ligand binding domain co-bound to heme and ncor ID1 peptide
6WMQ · Nuclear receptor rev-erba beta variant 1: “Crystal structure of human rev-erbbeta ligand binding domain co-bound to heme and ncor ID1 peptide”. X-ray diffraction, 1 ligand (HEM), 6 pockets (best druggability 0.81). MolNFT v1 #168640…
- PDB
- 6WMQ
- Type
- protein
- Length
- 423 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor rev-erba beta variant 1; Nuclear receptor corepressor 1
- UniProt
- F1D8P2, O75376
- Ligands
- HEM
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nuclear receptor rev-erba beta variant 1 | protein | 197 | 69% helix, 4% strand | F1D8P2 |
| E | Nuclear receptor corepressor 1 | protein | 15 | 40% helix, 0% strand | O75376 |
| F | Nuclear receptor corepressor 1 | protein | 14 | 43% helix, 0% strand | O75376 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, E, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.81 | 0.82 | 83 | HEM |
| 2 | 319 | 0.78 | 0.88 | 43 | HEM |
| 3 | 114 | 0.72 | 0.93 | 19 | empty |
| 4 | 128 | 0.58 | 0.84 | 27 | empty |
| 5 | 99 | 0.45 | 0.79 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1174 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 697 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 691 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 53 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 43 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6WMQ · Crystal Structure of Human REV-ERBbeta Ligand Binding Domain Co-Bound to Heme and NCoR… · the same entry in another collection · chain A against A, TM-score 1.00
- O75376 · AlphaFold monomer V2.0 prediction for nuclear receptor corepressor 1 (O75376) · a predicted model of the same protein · chain E against A, TM-score 0.42
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 F1D8P2
- Every structure of UniProt O75376
- Elsewhere: RCSB PDB 6WMQ · PDBe 6WMQ · UniProt F1D8P2 · UniProt O75376
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