MolNFT v1 · #135917 · protein
Crystal structure of rsv F A2 bound to MEDI8897
5UDC · MEDI8897 Fab heavy chain: “Crystal structure of rsv F A2 bound to MEDI8897”. X-ray diffraction, 4 ligands (MAN, NAG, BMA), 20 pockets (best druggability 0.83). MolNFT v1 #135917 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5UDC
- Type
- protein
- Length
- 2,635 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MEDI8897 Fab heavy chain; MEDI8897 Fab light chain; Fusion glycoprotein F0
- UniProt
- P03420
- Ligands
- MAN, NAG, BMA, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 21% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | MEDI8897 Fab heavy chain | protein | 217 | 6% helix, 53% strand | — |
| L, C | MEDI8897 Fab light chain | protein | 211 | 6% helix, 52% strand | — |
| F | Fusion glycoprotein F0 | protein | 449 | 33% helix, 34% strand | P03420 |
| B | MEDI8897 Fab heavy chain | protein | 218 | 7% helix, 52% strand | — |
| A | Fusion glycoprotein F0 | protein | 448 | 32% helix, 33% strand | P03420 |
| E | MEDI8897 Fab heavy chain | protein | 220 | 7% helix, 53% strand | — |
| G | MEDI8897 Fab light chain | protein | 213 | 6% helix, 52% strand | — |
| D | Fusion glycoprotein F0 | protein | 448 | 33% helix, 34% strand | P03420 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains H, F
- BMA · beta-D-mannopyranose · sugar · chains H
- CL · Chloride ion · ion · 2 copies · chains F, A
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 | 875 | 0.83 | 0.85 | 79 | empty |
| 2 | 465 | 0.78 | 0.86 | 51 | empty |
| 3 | 1071 | 0.74 | 0.77 | 92 | empty |
| 4 | 574 | 0.74 | 0.81 | 68 | empty |
| 5 | 736 | 0.72 | 0.78 | 60 | empty |
Interfaces
15 interfaces between chains.
- F–A · 2209 Ų buried · 19 hydrogen bonds · protein-protein
- F–D · 2188 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 2145 Ų buried · 27 hydrogen bonds · protein-protein
- H–L · 1725 Ų buried · 8 hydrogen bonds · protein-protein
- E–G · 1687 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5UDC · Crystal Structure of RSV F A2 Bound to MEDI8897 · the same entry in another collection · chain L against L, 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 5UDC · PDBe 5UDC · UniProt P03420
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