Research workbench
Crystal structure of bone morphogenetic protein 1 protease domain in complex with partially bound dmso
Analyse Crystal structure of bone morphogenetic protein 1 protease domain in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EDH
- Type
- protein
- Length
- 201 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bone morphogenetic protein 1
- EC
- 3.4.24.19
- UniProt
- P13497
- Ligands
- ACE, ZN
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bone morphogenetic protein 1 (EC 3.4.24.19) | protein | 201 | 32% helix, 18% strand | P13497 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.44 | 0.76 | 21 | ZN, DMS |
| 2 | 77 | 0.36 | 0.76 | 18 | empty |
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 3EDH · Crystal structure of bone morphogenetic protein 1 protease domain in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P13497 · AlphaFold monomer V2.0 prediction for bone morphogenetic protein 1 (P13497) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P13497
- Elsewhere: RCSB PDB 3EDH · PDBe 3EDH · UniProt P13497
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