MolNFT v1 · #40676 · protein
Gramicidin D complex with ki
2IZQ: “Gramicidin D complex with ki”. X-ray diffraction, 3 ligands (ETA, K, IOD). MolNFT v1 #40676 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2IZQ
- Type
- protein
- Length
- 60 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gramicidin D
- Ligands
- ETA, K, IOD
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 87% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Gramicidin D | protein | 15 | 0% helix, 87% strand | — |
Ligands and binding sites
- ETA · Ethanolamine · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 6 copies · chains A, B, C, D
- IOD · Iodide ion · ion · 8 copies · chains A, B, C, D
- MOH · Methanol · additive · 7 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
6 interfaces between chains.
- A–B · 1191 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1187 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 191 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 179 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 142 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 d-amino, 4 covalent, 4 modified (D-amino acid, covalent ligand, nonstandard).
Compared structures
- 2IZQ · Gramicidin D complex with KI · 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
- Elsewhere: RCSB PDB 2IZQ · PDBe 2IZQ
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