Research workbench
Crystal structure of the carbohydrate recognition domain of LMAN1 in complex with MCFD2
Analyse Crystal structure of the carbohydrate recognition domain of LMAN1 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LCP
- Type
- protein
- Length
- 605 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein ergic-53; Multiple coagulation factor deficiency protein 2
- UniProt
- P49257, Q8NI22
- Ligands
- CA
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein ergic-53 | protein | 234 | 1% helix, 47% strand | P49257 |
| C | Multiple coagulation factor deficiency protein 2 | protein | 68 | 56% helix, 3% strand | Q8NI22 |
| D | Multiple coagulation factor deficiency protein 2 | protein | 69 | 57% helix, 6% strand | Q8NI22 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.60 | 0.89 | 22 | empty |
| 2 | 75 | 0.54 | 0.86 | 24 | empty |
| 3 | 224 | 0.47 | 0.74 | 42 | empty |
| 4 | 180 | 0.45 | 0.74 | 26 | empty |
| 5 | 151 | 0.41 | 0.74 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–D · 897 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 887 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 652 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3LCP · Crystal structure of the carbohydrate recognition domain of LMAN1 in complex with MCFD2 · the same entry in another collection · chain A against A, TM-score 1.00
- P49257 · AlphaFold monomer V2.0 prediction for protein ergic-53 (P49257) · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q8NI22 · AlphaFold monomer V2.0 prediction for multiple coagulation factor deficiency protein 2… · a predicted model of the same protein · chain D against A, TM-score 0.93
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 P49257
- Every structure of UniProt Q8NI22
- Elsewhere: RCSB PDB 3LCP · PDBe 3LCP · UniProt P49257 · UniProt Q8NI22
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