MolNFT v1 · #134346 · protein
Crystal structure of EBV GHGL/GP42/E1D1 complex
5T1D · Envelope glycoprotein H: “Crystal structure of EBV GHGL/GP42/E1D1 complex”. X-ray diffraction, 1 ligand (NAG), 19 pockets (best druggability 0.76). MolNFT v1 #134346 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5T1D
- Type
- protein
- Length
- 1,356 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein H; Envelope glycoprotein L; Glycoprotein 42; E1D1 IGG2A heavy…
- UniProt
- P03231, P03212, P0C6Z5
- Ligands
- NAG
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein H | protein | 650 | 36% helix, 19% strand | P03231 |
| B | Envelope glycoprotein L | protein | 99 | 32% helix, 16% strand | P03212 |
| C | Glycoprotein 42 | protein | 177 | 9% helix, 16% strand | P0C6Z5 |
| H | E1D1 IGG2A heavy chain | protein | 213 | 1% helix, 46% strand | — |
| L | E1D1 IGG2A light chain | protein | 217 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.76 | 0.94 | 23 | empty |
| 2 | 557 | 0.70 | 0.79 | 62 | empty |
| 3 | 211 | 0.61 | 0.82 | 25 | empty |
| 4 | 102 | 0.55 | 0.84 | 18 | empty |
| 5 | 303 | 0.54 | 0.75 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2663 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2218 Ų buried · 22 hydrogen bonds · protein-protein
- H–L · 1687 Ų buried · 10 hydrogen bonds · protein-protein
- B–H · 760 Ų buried · 10 hydrogen bonds · protein-protein
- B–L · 346 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5T1D · Crystal structure of EBV gHgL/gp42/E1D1 complex · the same entry in another collection · chain A against A, TM-score 1.00
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 P03231
- Every structure of UniProt P03212
- Every structure of UniProt P0C6Z5
- Elsewhere: RCSB PDB 5T1D · PDBe 5T1D · UniProt P03231 · UniProt P03212 · UniProt P0C6Z5
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