Research workbench

Human surfactant protein D

Analyse Human surfactant protein D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DBZ
Type: protein
Length: 457 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pulmonary surfactant-associated protein D
UniProt: P35247
Ligands: CA
Pockets: 4 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pulmonary surfactant-associated protein D	protein	152	35% helix, 25% strand	P35247
B	Pulmonary surfactant-associated protein D	protein	155	37% helix, 28% strand	P35247
C	Pulmonary surfactant-associated protein D	protein	150	36% helix, 25% strand	P35247

Ligands and binding sites

CA · Calcium ion · metal · 9 copies · chains A, B, C
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	208	0.59	0.81	33	empty
2	133	0.52	0.80	21	empty
3	166	0.47	0.76	22	empty
4	137	0.47	0.77	23	empty

Interfaces

3 interfaces between chains.

B–C · 1173 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1139 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1121 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3DBZ · human surfactant protein D · 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 A 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 3DBZ · PDBe 3DBZ · UniProt P35247

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