MolNFT v1 · #115008 · protein
Crystal structure of hcmv glycoprotein B in complex with 1G2 Fab
5C6T · Envelope glycoprotein B: “Crystal structure of hcmv glycoprotein B in complex with 1G2 Fab”. X-ray diffraction, 2 ligands (NAG, MG), 8 pockets (best druggability 0.58). MolNFT v1 #115008 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5C6T
- Type
- protein
- Length
- 783 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein B; 1G2 Fab heavy chain; 1G2 Fab light chain
- UniProt
- P13201
- Ligands
- NAG, MG
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein B | protein | 566 | 18% helix, 34% strand | P13201 |
| H | 1G2 Fab heavy chain | protein | 113 | 3% helix, 47% strand | — |
| L | 1G2 Fab light chain | protein | 104 | 3% helix, 34% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, L, H
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.58 | 0.89 | 19 | empty |
| 2 | 233 | 0.52 | 0.76 | 33 | empty |
| 3 | 193 | 0.52 | 0.77 | 31 | empty |
| 4 | 151 | 0.46 | 0.76 | 23 | empty |
| 5 | 140 | 0.42 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- H–L · 809 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 693 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 88 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 glycan, 7 disulfide (N-glycosylation, disulfide).
Compared structures
- 5C6T · Crystal structure of HCMV glycoprotein B in complex with 1G2 Fab · 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 P13201
- Elsewhere: RCSB PDB 5C6T · PDBe 5C6T · UniProt P13201
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