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N-terminal domain of mouse surfactant protein B with bound lipid, Y59A/H79A mutant
Analyse N-terminal domain of mouse surfactant protein B with bound lipid, Y59A/H79A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W1B
- Type
- protein
- Length
- 629 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pulmonary surfactant-associated protein B
- UniProt
- P50405
- Ligands
- PEE
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, H | Pulmonary surfactant-associated protein B | protein | 78 | 78% helix, 0% strand | P50405 |
| E | Pulmonary surfactant-associated protein B | protein | 81 | 74% helix, 0% strand | P50405 |
| B | Pulmonary surfactant-associated protein B | protein | 77 | 78% helix, 0% strand | P50405 |
| C | Pulmonary surfactant-associated protein B | protein | 80 | 76% helix, 0% strand | P50405 |
| D | Pulmonary surfactant-associated protein B | protein | 79 | 76% helix, 0% strand | P50405 |
| G | Pulmonary surfactant-associated protein B | protein | 78 | 74% helix, 0% strand | P50405 |
Ligands and binding sites
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 13 copies · chains A, E, D, F, B, C, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.75 | 0.79 | 60 | PEE |
| 2 | 681 | 0.75 | 0.79 | 58 | PEE |
| 3 | 731 | 0.71 | 0.77 | 57 | PEE |
| 4 | 390 | 0.68 | 0.79 | 41 | empty |
| 5 | 155 | 0.62 | 0.84 | 18 | empty |
Interfaces
15 interfaces between chains.
- D–F · 1040 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 1001 Ų buried · 0 hydrogen bonds · protein-protein
- G–H · 992 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 954 Ų buried · 0 hydrogen bonds · protein-protein
- E–B · 315 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 6W1B · N-terminal domain of mouse surfactant protein B with bound lipid, Y59A/H79A mutant · the same entry in another collection · chain H against H, 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 6W1B · PDBe 6W1B · UniProt P50405
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