Research workbench
Complex of 3'-sulfo-lewis-X with a selectin-like mutant of mannose- binding protein a
Analyse Complex of 3'-sulfo-lewis-X with a selectin-like mutant of mannose- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KMB
- Type
- protein
- Length
- 447 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannose-binding protein-a
- UniProt
- P19999
- Ligands
- SGA, FUC, MAG, NAG, CA, CL
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 2, 3 | Mannose-binding protein-a | protein | 149 | 36% helix, 26% strand | P19999 |
Ligands and binding sites
- SGA · 3-O-sulfo-beta-D-galactopyranose · ligand · 2 copies · chains 1, 3
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains 1, 3, 2
- MAG · methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside · sugar · chains 1
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains 3
- CA · Calcium ion · metal · 10 copies · chains 1, 2, 3
- CL · Chloride ion · ion · 3 copies · chains 1, 2, 3
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.71 | 0.75 | 86 | empty |
| 2 | 243 | 0.57 | 0.78 | 28 | empty |
| 3 | 267 | 0.56 | 0.77 | 30 | CA |
Interfaces
3 interfaces between chains.
- 1–2 · 1070 Ų buried · 7 hydrogen bonds · protein-protein
- 2–3 · 1061 Ų buried · 7 hydrogen bonds · protein-protein
- 1–3 · 1046 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3KMB · Complex of 3'-sulfo-lewis-X with a selectin-like mutant of mannose-binding protein a · the same entry in another collection · chain 1 against 1, TM-score 1.00
- P19999 · AlphaFold monomer V2.0 prediction for mannose-binding protein a (P19999) · a predicted model of the same protein · chain 1 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 P19999
- Elsewhere: RCSB PDB 3KMB · PDBe 3KMB · UniProt P19999
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