MolNFT v1 · #118488 · protein
Structure of myostatin in complex with chimeric RK35 antibody
5F3B · RK35 chimeric antibody heavy chain: “Structure of myostatin in complex with chimeric RK35 antibody”. X-ray diffraction, 13 pockets (best druggability 0.66). MolNFT v1 #118488 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5F3B
- Type
- protein
- Length
- 1,070 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RK35 chimeric antibody heavy chain; RK35 chimeric antibody light chain…
- UniProt
- O14793
- Pockets
- 13 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RK35 chimeric antibody heavy chain | protein | 218 | 8% helix, 49% strand | — |
| B, F | RK35 chimeric antibody light chain | protein | 213 | 6% helix, 50% strand | — |
| E | RK35 chimeric antibody heavy chain | protein | 217 | 8% helix, 49% strand | — |
| C | GROWTH/DIFFERENTIATION factor 8 | protein | 106 | 16% helix, 46% strand | O14793 |
| D | GROWTH/DIFFERENTIATION factor 8 | protein | 103 | 17% helix, 46% strand | O14793 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.66 | 0.76 | 68 | GOL |
| 2 | 591 | 0.65 | 0.76 | 45 | empty |
| 3 | 365 | 0.59 | 0.76 | 40 | GOL |
| 4 | 255 | 0.57 | 0.78 | 39 | empty |
| 5 | 237 | 0.54 | 0.77 | 34 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1808 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1767 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1730 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 705 Ų buried · 8 hydrogen bonds · protein-protein
- E–D · 705 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 5F3B · Structure of myostatin in complex with chimeric RK35 antibody · the same entry in another collection · chain D against D, TM-score 1.00
- O14793 · AlphaFold monomer V2.0 prediction for GROWTH/DIFFERENTIATION factor 8 (O14793) · a predicted model of the same protein · chain D against A, TM-score 0.79
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 O14793
- Elsewhere: RCSB PDB 5F3B · PDBe 5F3B · UniProt O14793
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