MolNFT v1 · #179695 · protein
Hcmv postfusion gb in complex with SM5-1 Fab
7KDD · Envelope glycoprotein B: “Hcmv postfusion gb in complex with SM5-1 Fab”. Electron microscopy, 2 ligands (NAG, CA), 20 pockets (best druggability 0.83). MolNFT v1 #179695 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KDD
- Type
- protein
- Length
- 2,436 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein B; SM5-1 Fab antibody heavy chain; SM5-1 Fab antibody light chain
- UniProt
- P13201
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Envelope glycoprotein B | protein | 571 | 18% helix, 35% strand | P13201 |
| D, F, H | SM5-1 Fab antibody heavy chain | protein | 131 | 2% helix, 37% strand | — |
| E, G, I | SM5-1 Fab antibody light chain | protein | 110 | 0% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, D, I, B, F, E, C, H, G
- CA · Calcium ion · metal · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.83 | 0.88 | 71 | empty |
| 2 | 1025 | 0.76 | 0.78 | 95 | empty |
| 3 | 703 | 0.75 | 0.80 | 66 | empty |
| 4 | 655 | 0.75 | 0.81 | 74 | empty |
| 5 | 62 | 0.73 | 0.98 | 19 | CA |
Interfaces
15 interfaces between chains.
- B–C · 6133 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 6106 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 6069 Ų buried · 52 hydrogen bonds · protein-protein
- D–E · 753 Ų buried · 4 hydrogen bonds · protein-protein
- F–G · 751 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 glycan, 18 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KDD · HCMV postfusion gB in complex with SM5-1 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 7KDD · PDBe 7KDD · UniProt P13201
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