Research workbench
Structural basis for the recognition of human cytomegalovirus glycoprotein B by the neutralizing human antibody SM5-1
Analyse Structural basis for the recognition of human cytomegalovirus glycoprotein B by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OT1
- Type
- protein
- Length
- 559 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein B; SM5-1 Fab heavy chain; SM5-1 Fab light chain
- UniProt
- P13201
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein B | protein | 113 | 16% helix, 49% strand | P13201 |
| H | SM5-1 Fab heavy chain | protein | 232 | 8% helix, 53% strand | — |
| L | SM5-1 Fab light chain | protein | 214 | 7% helix, 51% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, H, L
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.59 | 0.81 | 27 | empty |
| 2 | 306 | 0.55 | 0.75 | 32 | EDO |
| 3 | 235 | 0.48 | 0.74 | 34 | empty |
| 4 | 126 | 0.44 | 0.77 | 29 | empty |
| 5 | 78 | 0.40 | 0.79 | 25 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1747 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 537 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 282 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4OT1 · Structural Basis for the Recognition of Human Cytomegalovirus Glycoprotein B by the… · 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 4OT1 · PDBe 4OT1 · UniProt P13201
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