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N-terminal domain of mouse surfactant protein B (K46E/R51E mutant) with bound lipid
Analyse N-terminal domain of mouse surfactant protein B (K46E/R51E mutant) with bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VZD
- Type
- protein
- Length
- 320 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pulmonary surfactant-associated protein B
- UniProt
- P50405
- Ligands
- RXY
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pulmonary surfactant-associated protein B | protein | 79 | 73% helix, 0% strand | P50405 |
| E | Pulmonary surfactant-associated protein B | protein | 85 | 71% helix, 0% strand | P50405 |
| B, C | Pulmonary surfactant-associated protein B | protein | 78 | 73% helix, 0% strand | P50405 |
Ligands and binding sites
- RXY · (7Z,19R,22R)-25-amino-22-hydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphapentacos-7-en-19-yl (9Z)-octadec-9-enoate · ligand · 6 copies · chains A, E, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.75 | 0.76 | 58 | RXY |
| 2 | 997 | 0.75 | 0.76 | 56 | RXY |
| 3 | 84 | 0.74 | 0.97 | 29 | empty |
| 4 | 150 | 0.40 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–E · 1192 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 1120 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 739 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6VZD · N-terminal domain of mouse surfactant protein B (K46E/R51E mutant) with bound lipid · the same entry in another collection · chain A against A, TM-score 1.00
- P50405 · AlphaFold monomer V2.0 prediction for pulmonary surfactant-associated protein B (P50405) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P50405
- Elsewhere: RCSB PDB 6VZD · PDBe 6VZD · UniProt P50405
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