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Crystal structure of surfactant protein-D D325A/R343V mutant in complex with trimannose (man-A1,2MAN-A1,2MAN)
Analyse Crystal structure of surfactant protein-D D325A/R343V mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M18
- Type
- protein
- Length
- 1,721 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pulmonary surfactant-associated protein D
- UniProt
- P35247
- Ligands
- MAN, CA
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, I, J | Pulmonary surfactant-associated protein D | protein | 142 | 32% helix, 28% strand | P35247 |
| C | Pulmonary surfactant-associated protein D | protein | 144 | 33% helix, 28% strand | P35247 |
| D, E, F, H | Pulmonary surfactant-associated protein D | protein | 145 | 33% helix, 27% strand | P35247 |
| G, K, L | Pulmonary surfactant-associated protein D | protein | 143 | 32% helix, 27% strand | P35247 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 34 copies · chains A, E, B, C, D, L, F, H, G, I, J, K
- CA · Calcium ion · metal · 38 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.81 | 0.83 | 124 | empty |
| 2 | 994 | 0.78 | 0.80 | 125 | empty |
| 3 | 1063 | 0.77 | 0.79 | 121 | empty |
| 4 | 152 | 0.62 | 0.85 | 32 | empty |
| 5 | 192 | 0.60 | 0.83 | 31 | empty |
Interfaces
21 interfaces between chains.
- D–E · 949 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 927 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 927 Ų buried · 9 hydrogen bonds · protein-protein
- G–I · 927 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 899 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 4M18 · Crystal Structure of Surfactant Protein-D D325A/R343V mutant in complex with trimannose… · the same entry in another collection · 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 4M18 · PDBe 4M18 · UniProt P35247
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