MolNFT v1 · #176126 · protein
Cryo-EM structure of human XKR8-basigin complex bound to Fab fragment
7DCE · Isoform 2 of basigin: “Cryo-EM structure of human XKR8-basigin complex bound to Fab fragment”. Electron microscopy, 1 ligand (DLP), 13 pockets (best druggability 0.64). MolNFT v1 #176126 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7DCE
- Type
- protein
- Length
- 912 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2 of basigin; Xk-related protein 8; Heavy chain of Fab fragment; Light chain of…
- UniProt
- P35613, Q9H6D3
- Ligands
- DLP
- Pockets
- 13 · best druggability 0.64
Structure
electron microscopy · 4 distinct chains · 36% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Isoform 2 of basigin | protein | 132 | 20% helix, 45% strand | P35613 |
| X | Xk-related protein 8 | protein | 354 | 75% helix, 0% strand | Q9H6D3 |
| H | Heavy chain of Fab fragment | protein | 209 | 8% helix, 53% strand | — |
| L | Light chain of Fab fragment | protein | 217 | 9% helix, 52% strand | — |
Ligands and binding sites
- DLP · 1,2-dilinoleoyl-sn-glycero-3-phosphocholine · ligand · chains X, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 656 | 0.64 | 0.75 | 71 | empty |
| 2 | 316 | 0.63 | 0.79 | 36 | DLP |
| 3 | 220 | 0.58 | 0.80 | 32 | empty |
| 4 | 111 | 0.58 | 0.84 | 16 | empty |
| 5 | 88 | 0.45 | 0.80 | 22 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1732 Ų buried · 7 hydrogen bonds · protein-protein
- B–X · 946 Ų buried · 5 hydrogen bonds · protein-protein
- B–L · 625 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 441 Ų buried · 3 hydrogen bonds · protein-protein
- X–L · 276 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 7DCE · Cryo-EM structure of human XKR8-basigin complex bound to Fab fragment · the same entry in another collection · chain L against L, TM-score 1.00
- Q9H6D3 · AlphaFold monomer V2.0 prediction for xk-related protein 8 (Q9H6D3) · a predicted model of the same protein · chain X against A, TM-score 0.92
- P35613 · AlphaFold monomer V2.0 prediction for basigin (P35613) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 P35613
- Every structure of UniProt Q9H6D3
- Elsewhere: RCSB PDB 7DCE · PDBe 7DCE · UniProt P35613 · UniProt Q9H6D3
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