Research workbench
Crystal structure of geodia cydonium BHP2 in complex with lubomirskia baicalensis bak-2
Analyse Crystal structure of geodia cydonium BHP2 in complex with lubomirskia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TWA
- Type
- protein
- Length
- 369 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCL-X homologous protein, BHP2; Bak-2 protein
- UniProt
- Q967D2, Q1RPT5
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCL-X homologous protein, BHP2 | protein | 161 | 74% helix, 0% strand | Q967D2 |
| D, C | Bak-2 protein | protein | 25 | 88% helix, 0% strand | Q1RPT5 |
| B | BCL-X homologous protein, BHP2 | protein | 158 | 75% helix, 0% strand | Q967D2 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, D, B, C
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.32 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1034 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1016 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5TWA · Crystal structure of Geodia cydonium BHP2 in complex with Lubomirskia baicalensis Bak-2 · 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 Q967D2
- Every structure of UniProt Q1RPT5
- Elsewhere: RCSB PDB 5TWA · PDBe 5TWA · UniProt Q967D2 · UniProt Q1RPT5
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