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Crystal structure of the activin receptor type-2B ligand binding domain in complex with bimagrumab fv, orthorhombic crystal form
Analyse Crystal structure of the activin receptor type-2B ligand binding domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NGV
- Type
- protein
- Length
- 319 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activin receptor type-2B; Anti-human actriib mab BYM338 heavy-chain; Anti-human actriib…
- EC
- 2.7.11.30
- UniProt
- Q13705
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activin receptor type-2B (EC 2.7.11.30) | protein | 93 | 11% helix, 46% strand | Q13705 |
| H | Anti-human actriib mab BYM338 heavy-chain | protein | 114 | 8% helix, 49% strand | — |
| L | Anti-human actriib mab BYM338 light-chain | protein | 112 | 3% helix, 45% strand | — |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.63 | 0.86 | 22 | PG4 |
| 2 | 82 | 0.41 | 0.79 | 20 | empty |
| 3 | 52 | 0.31 | 0.77 | 16 | empty |
| 4 | 72 | 0.30 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 851 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 784 Ų buried · 11 hydrogen bonds · protein-protein
- A–L · 394 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 5NGV · CRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING DOMAIN IN COMPLEX WITH… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13705 · AlphaFold monomer V2.0 prediction for activin receptor type-2B (Q13705) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q13705
- Elsewhere: RCSB PDB 5NGV · PDBe 5NGV · UniProt Q13705
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