Research workbench
Crystal structure of rsv F in complex with 5C4 Fab
Analyse Crystal structure of rsv F in complex with 5C4 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W23
- Type
- protein
- Length
- 2,646 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0; 5C4 Fab heavy chain; 5C4 Fab light chain
- UniProt
- P03420
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 23% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusion glycoprotein F0 | protein | 446 | 31% helix, 32% strand | P03420 |
| B | Fusion glycoprotein F0 | protein | 448 | 32% helix, 33% strand | P03420 |
| C | Fusion glycoprotein F0 | protein | 449 | 31% helix, 33% strand | P03420 |
| H, I, J | 5C4 Fab heavy chain | protein | 219 | 5% helix, 51% strand | — |
| L | 5C4 Fab light chain | protein | 216 | 6% helix, 53% strand | — |
| M, N | 5C4 Fab light chain | protein | 215 | 6% helix, 55% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, C, B, H, I, J, N
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 | 940 | 0.82 | 0.83 | 71 | empty |
| 2 | 938 | 0.81 | 0.83 | 69 | empty |
| 3 | 605 | 0.74 | 0.81 | 58 | empty |
| 4 | 677 | 0.72 | 0.79 | 61 | empty |
| 5 | 398 | 0.71 | 0.83 | 41 | empty |
Interfaces
14 interfaces between chains.
- A–C · 2323 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 2179 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 2147 Ų buried · 24 hydrogen bonds · protein-protein
- H–L · 1951 Ų buried · 20 hydrogen bonds · protein-protein
- I–M · 1937 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide (disulfide).
Compared structures
- 5W23 · Crystal Structure of RSV F in complex with 5C4 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 P03420
- Elsewhere: RCSB PDB 5W23 · PDBe 5W23 · UniProt P03420
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