Research workbench
Structural states of rorgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds
Analyse Structural states of rorgt: X-ray elucidation of molecular mechanisms and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NTI
- 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; Asn-ser-his-gln-lys-val-thr-leu-leu-gln-leu-leu-leu-gly…
- UniProt
- P51449
- Ligands
- C3S
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nuclear receptor ror-gamma | protein | 245 | 71% helix, 4% strand | P51449 |
| B, D | Nuclear receptor ror-gamma | protein | 244 | 73% helix, 4% strand | P51449 |
| P, Q, R | Asn-ser-his-gln-lys-val-thr-leu-leu-gln-leu-leu-leu-gly- his-lys-asn-glu-glu-asn | protein | 8 | 75% helix, 0% strand | — |
| S | Asn-ser-his-gln-lys-val-thr-leu-leu-gln-leu-leu-leu-gly- his-lys-asn-glu-glu-asn | protein | 9 | 67% helix, 0% strand | — |
Ligands and binding sites
- C3S · Cholest-5-en-3-yl hydrogen sulfate · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.90 | 0.91 | 93 | C3S |
| 2 | 618 | 0.87 | 0.91 | 50 | C3S |
| 3 | 640 | 0.87 | 0.91 | 56 | C3S |
| 4 | 536 | 0.65 | 0.77 | 58 | empty |
| 5 | 149 | 0.53 | 0.80 | 21 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1254 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 868 Ų buried · 13 hydrogen bonds · protein-protein
- D–S · 496 Ų buried · 4 hydrogen bonds · protein-protein
- B–Q · 475 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 469 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5NTI · Structural states of RORgt: X-ray elucidation of molecular mechanisms and binding… · 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 P51449
- Elsewhere: RCSB PDB 5NTI · PDBe 5NTI · UniProt P51449
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