MolNFT v1 · #160203 · protein
Crystal structure of hendra virus attachment G glycoprotein in complex with receptor ephrin-B2
6PDL · Attachment glycoprotein: “Crystal structure of hendra virus attachment G glycoprotein in complex with receptor ephrin-B2”. X-ray diffraction, 4 ligands (NAG, FUC, BMA), 20 pockets (best druggability 0.81). MolNFT v1 #160203 on…
- PDB
- 6PDL
- Type
- protein
- Length
- 2,222 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Attachment glycoprotein; Ephrin-B2
- UniProt
- F4YH71, P52799
- Ligands
- NAG, FUC, BMA, MAN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Attachment glycoprotein | protein | 421 | 4% helix, 48% strand | F4YH71 |
| B, F | Ephrin-B2 | protein | 133 | 11% helix, 35% strand | P52799 |
| C, G | Attachment glycoprotein | protein | 418 | 4% helix, 48% strand | F4YH71 |
| D, H | Ephrin-B2 | protein | 139 | 11% helix, 33% strand | P52799 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 37 copies · chains A, B, C, D, E, H, F, G
- FUC · alpha-L-fucopyranose · sugar · 8 copies · chains A, B, C, D, E, F, G, H
- BMA · beta-D-mannopyranose · sugar · 6 copies
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.81 | 0.88 | 56 | empty |
| 2 | 475 | 0.81 | 0.88 | 46 | empty |
| 3 | 472 | 0.80 | 0.88 | 46 | empty |
| 4 | 497 | 0.80 | 0.87 | 44 | empty |
| 5 | 728 | 0.67 | 0.75 | 72 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1393 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1385 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1337 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1334 Ų buried · 20 hydrogen bonds · protein-protein
- C–H · 502 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 25 glycan (disulfide, N-glycosylation).
Compared structures
- 6PDL · Crystal Structure of Hendra Virus Attachment G Glycoprotein in Complex with Receptor… · the same entry in another collection · chain H against H, TM-score 1.00
- P52799 · AlphaFold monomer V2.0 prediction for ephrin-B2 (P52799) · a predicted model of the same protein · chain F against A, TM-score 0.96
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 F4YH71
- Every structure of UniProt P52799
- Elsewhere: RCSB PDB 6PDL · PDBe 6PDL · UniProt F4YH71 · UniProt P52799
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