Research workbench
Crystal structure of the activin receptor type-2A ligand binding domain in complex with bimagrumab fv
Analyse Crystal structure of the activin receptor type-2A 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
- 5NH3
- Type
- protein
- Length
- 639 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activin receptor type-2A; Anti-human actriib mab BYM338 fv heavy-chain; Anti-human…
- EC
- 2.7.11.30
- UniProt
- P27037
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activin receptor type-2A (EC 2.7.11.30) | protein | 94 | 7% helix, 44% strand | P27037 |
| B | Activin receptor type-2A (EC 2.7.11.30) | protein | 95 | 7% helix, 43% strand | P27037 |
| H, I | Anti-human actriib mab BYM338 fv heavy-chain | protein | 114 | 11% helix, 49% strand | — |
| L, M | Anti-human actriib mab BYM338 fv light-chain | protein | 111 | 3% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.60 | 0.77 | 47 | empty |
| 2 | 220 | 0.60 | 0.81 | 27 | empty |
| 3 | 360 | 0.57 | 0.75 | 49 | empty |
| 4 | 231 | 0.53 | 0.77 | 39 | empty |
| 5 | 84 | 0.43 | 0.79 | 20 | empty |
Interfaces
9 interfaces between chains.
- I–M · 811 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 800 Ų buried · 9 hydrogen bonds · protein-protein
- B–I · 650 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 630 Ų buried · 8 hydrogen bonds · protein-protein
- B–M · 269 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 5NH3 · CRYSTAL STRUCTURE OF THE Activin receptor type-2A LIGAND BINDING DOMAIN IN COMPLEX WITH… · the same entry in another collection · chain M against M, TM-score 1.00
- P27037 · AlphaFold monomer V2.0 prediction for activin receptor type-2A (P27037) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P27037
- Elsewhere: RCSB PDB 5NH3 · PDBe 5NH3 · UniProt P27037
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