MolNFT v1 · #50441 · protein
Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with L-glycero-D- manno-heptopyranosyl-(1-3)-L-glycero-D-manno-heptopyranose
2RIC · Pulmonary surfactant-associated protein D: “Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in…”. X-ray diffraction, 2 ligands (GMH, CA), 4 pockets (best druggability 0.60).…
- PDB
- 2RIC
- Type
- protein
- Length
- 465 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pulmonary surfactant-associated protein D
- UniProt
- P35247
- Ligands
- GMH, CA
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pulmonary surfactant-associated protein D | protein | 155 | 38% helix, 25% strand | P35247 |
| B | Pulmonary surfactant-associated protein D | protein | 152 | 37% helix, 25% strand | P35247 |
| C | Pulmonary surfactant-associated protein D | protein | 158 | 39% helix, 28% strand | P35247 |
Ligands and binding sites
- GMH · L-glycero-alpha-D-manno-heptopyranose · sugar · 5 copies · chains B, C, A
- 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 | 210 | 0.60 | 0.82 | 32 | empty |
| 2 | 140 | 0.49 | 0.78 | 22 | empty |
| 3 | 153 | 0.48 | 0.77 | 26 | empty |
| 4 | 118 | 0.45 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1202 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1170 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1062 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2RIC · 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 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 2RIC · PDBe 2RIC · UniProt P35247
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.