MolNFT v1 · #168642 · protein
Crystal structure of human rev-erbbeta ligand binding domain co-bound to heme and ncor ID2 peptide
6WMS · Nuclear receptor rev-erba beta variant 1: “Crystal structure of human rev-erbbeta ligand binding domain co-bound to heme and ncor ID2 peptide”. X-ray diffraction, 1 ligand (HEM), 5 pockets (best druggability 0.75). MolNFT v1 #168642…
- PDB
- 6WMS
- Type
- protein
- Length
- 415 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor rev-erba beta variant 1; Ncor isoform C
- UniProt
- F1D8P2, Q86YY1
- Ligands
- HEM
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nuclear receptor rev-erba beta variant 1 | protein | 196 | 68% helix, 4% strand | F1D8P2 |
| E | Ncor isoform C | protein | 11 | 82% helix, 0% strand | Q86YY1 |
| F | Ncor isoform C | protein | 12 | 75% helix, 0% strand | Q86YY1 |
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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.75 | 0.83 | 56 | HEM |
| 2 | 524 | 0.74 | 0.82 | 57 | HEM |
| 3 | 122 | 0.52 | 0.81 | 15 | empty |
| 4 | 65 | 0.39 | 0.79 | 13 | empty |
| 5 | 85 | 0.33 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1258 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 545 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 525 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6WMS · 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
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 Q86YY1
- Elsewhere: RCSB PDB 6WMS · PDBe 6WMS · UniProt F1D8P2 · UniProt Q86YY1
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