Research workbench
Crystal structure of a resiniferatoxin-binding protein from rhodobacter sphaeroides
Analyse Crystal structure of a resiniferatoxin-binding protein from rhodobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K2G
- Type
- protein
- Length
- 1,430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Resiniferatoxin-binding, phosphotriesterase-related protein
- UniProt
- Q3IVY4
- Ligands
- DTV, ZN, MG
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Resiniferatoxin-binding, phosphotriesterase-related protein | protein | 357 | 45% helix, 14% strand | Q3IVY4 |
| B, C | Resiniferatoxin-binding, phosphotriesterase-related protein | protein | 358 | 45% helix, 13% strand | Q3IVY4 |
| D | Resiniferatoxin-binding, phosphotriesterase-related protein | protein | 357 | 44% helix, 12% strand | Q3IVY4 |
Ligands and binding sites
- DTV · (2S,3S)-1,4-dimercaptobutane-2,3-diol · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.83 | 0.92 | 63 | empty |
| 2 | 437 | 0.80 | 0.88 | 73 | empty |
| 3 | 303 | 0.75 | 0.87 | 31 | DTV |
| 4 | 242 | 0.74 | 0.88 | 32 | DTV |
| 5 | 233 | 0.72 | 0.87 | 30 | DTV |
Interfaces
4 interfaces between chains.
- A–B · 1127 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1114 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 416 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 404 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified, 4 covalent (engineered, covalent ligand).
Compared structures
- 3K2G · Crystal structure of a Resiniferatoxin-binding protein from Rhodobacter sphaeroides · 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 Q3IVY4
- Elsewhere: RCSB PDB 3K2G · PDBe 3K2G · UniProt Q3IVY4
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