MolNFT v1 · #163634 · protein
Structure of the high affinity anticalin P3D11 in complex with the human CD98 heavy chain ectodomain
6S8V · Neutrophil gelatinase-associated lipocalin: “Structure of the high affinity anticalin P3D11 in complex with the human CD98 heavy chain ectodomain”. X-ray diffraction, 14 pockets (best druggability 0.84). MolNFT v1 #163634 on…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.