Research workbench
Crystal structure of human melanotransferrin in complex with SC57.32 Fab
Analyse Crystal structure of human melanotransferrin in complex with SC57.32 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XR0
- Type
- protein
- Length
- 1,112 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SC57.32 Fab heavy chain; SC57.32 Fab light chain; Melanotransferrin
- UniProt
- P08582
- Ligands
- BCT, NAG, MG, NA, FE
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | SC57.32 Fab heavy chain | protein | 215 | 6% helix, 51% strand | — |
| L | SC57.32 Fab light chain | protein | 214 | 6% helix, 50% strand | — |
| M | Melanotransferrin | protein | 683 | 33% helix, 18% strand | P08582 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · chains M
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains M, H
- MG · Magnesium ion · metal · chains M
- NA · Sodium ion · metal · chains M
- FE · Fe (III) ion · metal · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.74 | 0.89 | 45 | empty |
| 2 | 410 | 0.69 | 0.81 | 55 | empty |
| 3 | 305 | 0.54 | 0.75 | 38 | empty |
| 4 | 200 | 0.52 | 0.77 | 29 | NAG |
| 5 | 113 | 0.51 | 0.81 | 25 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1933 Ų buried · 16 hydrogen bonds · protein-protein
- H–M · 641 Ų buried · 16 hydrogen bonds · protein-protein
- L–M · 311 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6XR0 · Crystal Structure of Human Melanotransferrin in complex with SC57.32 Fab · the same entry in another collection · chain H against H, TM-score 1.00
- P08582 · AlphaFold monomer V2.0 prediction for melanotransferrin (P08582) · a predicted model of the same protein · chain M against A, TM-score 0.82
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 P08582
- Elsewhere: RCSB PDB 6XR0 · PDBe 6XR0 · UniProt P08582
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