MolNFT v1 · #128538 · protein
Structural states of rorgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds
5NTN · Nuclear receptor ror-gamma: “Structural states of rorgt: X-ray elucidation of molecular mechanisms and binding interactions for natural…”. X-ray diffraction, 1 ligand (98H), 20 pockets (best druggability 0.90). MolNFT v1 #128538 on…
- PDB
- 5NTN
- Type
- protein
- Length
- 1,011 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma; Nuclear receptor-interacting protein 1
- UniProt
- P51449, P48552
- Ligands
- 98H
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nuclear receptor ror-gamma | protein | 245 | 73% helix, 4% strand | P51449 |
| B, D | Nuclear receptor ror-gamma | protein | 244 | 73% helix, 4% strand | P51449 |
| P, Q, R | Nuclear receptor-interacting protein 1 | protein | 8 | 75% helix, 0% strand | P48552 |
| S | Nuclear receptor-interacting protein 1 | protein | 9 | 67% helix, 0% strand | P48552 |
Ligands and binding sites
- 98H · (5R,10S,13R,14R,17R)-17-((R,E)-7-hydroxy-6-methylhept-5-en-2-yl)-4,4,10,13,14-pentamethyl-1,2,5,6,10,11,12, 13,14,15,16,17-dodecahydro-3H-cyclopenta[a]phenanthrene-3,7(4H)-dione · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.90 | 0.91 | 94 | 98H |
| 2 | 1131 | 0.90 | 0.91 | 92 | 98H |
| 3 | 282 | 0.58 | 0.78 | 39 | empty |
| 4 | 144 | 0.54 | 0.81 | 20 | empty |
| 5 | 134 | 0.53 | 0.81 | 20 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1057 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 835 Ų buried · 13 hydrogen bonds · protein-protein
- D–S · 506 Ų buried · 5 hydrogen bonds · protein-protein
- B–Q · 487 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 478 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5NTN · Structural states of RORgt: X-ray elucidation of molecular mechanisms and binding… · the same entry in another collection · chain S against S, TM-score 1.00
- P48552 · AlphaFold monomer V2.0 prediction for nuclear receptor-interacting protein 1 (P48552) · a predicted model of the same protein · chain P against A, TM-score 0.93
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 P51449
- Every structure of UniProt P48552
- Elsewhere: RCSB PDB 5NTN · PDBe 5NTN · UniProt P51449 · UniProt P48552
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