Research workbench
Crystal structure of the cert start domain in complex with hpa-13
Analyse Crystal structure of the cert start domain in complex with hpa-13 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H3Q
- Type
- protein
- Length
- 470 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Goodpasture antigen binding protein
- UniProt
- A8K7S2
- Ligands
- H13
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Goodpasture antigen binding protein | protein | 236 | 25% helix, 38% strand | A8K7S2 |
| B | Goodpasture antigen binding protein | protein | 234 | 24% helix, 38% strand | A8K7S2 |
Ligands and binding sites
- H13 · N-[(1R,3R)-3-hydroxy-1-(hydroxymethyl)-3-phenylpropyl]tridecanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.86 | 0.94 | 46 | H13 |
| 2 | 356 | 0.85 | 0.94 | 44 | H13 |
| 3 | 661 | 0.70 | 0.78 | 52 | empty |
| 4 | 134 | 0.46 | 0.77 | 23 | empty |
| 5 | 92 | 0.38 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 526 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3H3Q · Crystal structure of the CERT START domain in complex with HPA-13 · the same entry in another collection · chain A against A, TM-score 1.00
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 A8K7S2
- Elsewhere: RCSB PDB 3H3Q · PDBe 3H3Q · UniProt A8K7S2
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