MolNFT v1 · #167892 · protein
N-terminal domain of mouse surfactant protein B with bound lipid, wild type
6VYN · Pulmonary surfactant-associated protein B: “N-terminal domain of mouse surfactant protein B with bound lipid, wild type”. X-ray diffraction, 1 ligand (RXY), 8 pockets (best druggability 0.75). MolNFT v1 #167892 on GenesisL1: 3D…
- PDB
- 6VYN
- Type
- protein
- Length
- 628 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pulmonary surfactant-associated protein B
- UniProt
- P50405
- Ligands
- RXY
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pulmonary surfactant-associated protein B | protein | 79 | 73% helix, 0% strand | P50405 |
| B, C, F | Pulmonary surfactant-associated protein B | protein | 79 | 73% helix, 0% strand | P50405 |
| D | Pulmonary surfactant-associated protein B | protein | 78 | 74% helix, 0% strand | P50405 |
| H | Pulmonary surfactant-associated protein B | protein | 77 | 75% helix, 0% strand | P50405 |
| E | Pulmonary surfactant-associated protein B | protein | 80 | 73% helix, 0% strand | P50405 |
| G | Pulmonary surfactant-associated protein B | protein | 77 | 74% 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 · 12 copies · chains A, E, B, C, D, F, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.75 | 0.77 | 60 | RXY |
| 2 | 998 | 0.75 | 0.77 | 58 | RXY |
| 3 | 1010 | 0.75 | 0.77 | 61 | RXY |
| 4 | 958 | 0.75 | 0.77 | 60 | RXY |
| 5 | 64 | 0.71 | 0.97 | 21 | empty |
Interfaces
7 interfaces between chains.
- D–F · 1169 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 1163 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 1146 Ų buried · 2 hydrogen bonds · protein-protein
- H–G · 1047 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 726 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 6VYN · N-terminal domain of mouse surfactant protein B with bound lipid, wild type · the same entry in another collection · chain G against G, 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 H against A, TM-score 0.99
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 6VYN · PDBe 6VYN · UniProt P50405
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