Research workbench
Structure of the high affinity anticalin P3D11 in complex with the human CD98 heavy chain ectodomain
Analyse Structure of the high affinity anticalin P3D11 in complex with the human CD98… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S8V
- Type
- protein
- Length
- 1,180 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin; 4F2 cell-surface antigen heavy chain
- UniProt
- P80188, P08195
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil gelatinase-associated lipocalin | protein | 172 | 13% helix, 41% strand | P80188 |
| B | 4F2 cell-surface antigen heavy chain | protein | 416 | 35% helix, 19% strand | P08195 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 172 | 11% helix, 41% strand | P80188 |
| D | 4F2 cell-surface antigen heavy chain | protein | 420 | 35% helix, 19% strand | P08195 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, D
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 | 1046 | 0.84 | 0.85 | 99 | empty |
| 2 | 260 | 0.72 | 0.86 | 36 | EDO |
| 3 | 488 | 0.70 | 0.80 | 46 | empty |
| 4 | 507 | 0.70 | 0.80 | 60 | empty |
| 5 | 79 | 0.69 | 0.94 | 21 | EDO |
Interfaces
4 interfaces between chains.
- A–B · 1542 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1409 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 661 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 500 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6S8V · Structure of the high affinity Anticalin P3D11 in complex with the human CD98 heavy chain… · the same entry in another collection · chain A against A, TM-score 1.00
- P08195 · AlphaFold monomer V2.0 prediction for 4F2 cell-surface antigen heavy chain (P08195) · 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 P80188
- Every structure of UniProt P08195
- Elsewhere: RCSB PDB 6S8V · PDBe 6S8V · UniProt P80188 · UniProt P08195
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