Research workbench
Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D- manno-heptose
Analyse Crystal structure of the trimeric neck and carbohydrate recognition domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RIA
- Type
- protein
- Length
- 438 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pulmonary surfactant-associated protein D
- UniProt
- P35247
- Ligands
- 289, CA
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Pulmonary surfactant-associated protein D | protein | 146 | 34% helix, 28% strand | P35247 |
Ligands and binding sites
- 289 · D-glycero-alpha-D-manno-heptopyranose · ligand · 3 copies · chains A, B, C
- 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.57 | 0.81 | 29 | empty |
| 2 | 144 | 0.48 | 0.78 | 22 | empty |
| 3 | 125 | 0.48 | 0.79 | 21 | empty |
| 4 | 134 | 0.46 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1012 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 985 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 976 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2RIA · Crystal structure of the trimeric neck and carbohydrate recognition domain of human… · 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 1.00
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 2RIA · PDBe 2RIA · UniProt P35247
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