MolNFT v1 · #128143 · protein
Crystal structure of the activin receptor type-2B ligand binding domain in complex with bimagrumab fv, cubic crystal form
5NHR · Bimagrumab fv light-chain: “Crystal structure of the activin receptor type-2B ligand binding domain in complex with bimagrumab fv, cubic…”. X-ray diffraction, 9 pockets (best druggability 0.59). MolNFT v1 #128143 on GenesisL1: 3D…
- PDB
- 5NHR
- Type
- protein
- Length
- 636 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bimagrumab fv light-chain; Bimagrumab fv heavy-chain; Activin receptor type-2B
- EC
- 2.7.11.30
- UniProt
- Q13705
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Bimagrumab fv light-chain | protein | 111 | 3% helix, 47% strand | — |
| H, A | Bimagrumab fv heavy-chain | protein | 115 | 5% helix, 50% strand | — |
| B | Bimagrumab fv light-chain | protein | 114 | 3% helix, 46% strand | — |
| C | Activin receptor type-2B (EC 2.7.11.30) | protein | 90 | 7% helix, 49% strand | Q13705 |
| D | Activin receptor type-2B (EC 2.7.11.30) | protein | 91 | 7% helix, 48% strand | Q13705 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.59 | 0.83 | 26 | empty |
| 2 | 152 | 0.58 | 0.83 | 27 | empty |
| 3 | 83 | 0.51 | 0.84 | 24 | empty |
| 4 | 73 | 0.50 | 0.85 | 24 | empty |
| 5 | 78 | 0.36 | 0.77 | 20 | empty |
Interfaces
6 interfaces between chains.
- B–A · 806 Ų buried · 9 hydrogen bonds · protein-protein
- L–H · 806 Ų buried · 7 hydrogen bonds · protein-protein
- H–C · 732 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 711 Ų buried · 8 hydrogen bonds · protein-protein
- L–C · 426 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5NHR · CRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING DOMAIN IN COMPLEX WITH… · the same entry in another collection · chain D against D, TM-score 1.00
- Q13705 · AlphaFold monomer V2.0 prediction for activin receptor type-2B (Q13705) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 5NHR · PDBe 5NHR · UniProt Q13705
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