Research workbench

Lung surfactant protein D (sp-D) (fragment)

Analyse Lung surfactant protein D (sp-D) (fragment) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1B08
Type: protein
Length: 451 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (lung surfactant protein D)
UniProt: P35247
Ligands: CA
Pockets: 4 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein (lung surfactant protein D)	protein	152	36% helix, 27% strand	P35247
B	Protein (lung surfactant protein D)	protein	151	36% helix, 26% strand	P35247
C	Protein (lung surfactant protein D)	protein	148	34% helix, 26% strand	P35247

Ligands and binding sites

CA · Calcium ion · metal · 9 copies · chains A, 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	202	0.59	0.81	34	empty
2	146	0.50	0.78	20	empty
3	99	0.49	0.81	21	empty
4	144	0.49	0.78	20	empty

Interfaces

3 interfaces between chains.

A–B · 1136 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 1080 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 1052 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

1B08 · Lung surfactant protein D (sp-D) (fragment) · the same entry in another collection · chain A against A, TM-score 1.00
P35247 · AlphaFold monomer V2.0 prediction for pulmonary surfactant-associated protein D (P35247) · a predicted model of the same protein · chain B 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 P35247
Elsewhere: RCSB PDB 1B08 · PDBe 1B08 · UniProt P35247

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