Research workbench
The structure of the bir domain of iap-like protein 2
Analyse The structure of the bir domain of iap-like protein 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XB1
- Type
- protein
- Length
- 593 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baculoviral iap repeat-containing protein 8; Diablo homolog, mitochondrial
- UniProt
- Q96P09, Q9NR28
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Baculoviral iap repeat-containing protein 8 | protein | 90 | 42% helix, 10% strand | Q96P09 |
| G, H, I, J, K, L | Diablo homolog, mitochondrial | protein | 5 | 0% helix, 40% strand | Q9NR28 |
| B, E | Baculoviral iap repeat-containing protein 8 | protein | 102 | 34% helix, 9% strand | Q96P09 |
| F | Baculoviral iap repeat-containing protein 8 | protein | 89 | 42% helix, 10% strand | Q96P09 |
Ligands and binding sites
- ZN · Zinc ion · metal · 23 copies · chains A, B, F, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.48 | 0.79 | 24 | ZN |
| 2 | 142 | 0.47 | 0.78 | 26 | ZN |
| 3 | 217 | 0.47 | 0.74 | 34 | empty |
| 4 | 186 | 0.46 | 0.75 | 33 | empty |
| 5 | 191 | 0.45 | 0.74 | 34 | ZN |
Interfaces
18 interfaces between chains.
- D–E · 539 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 524 Ų buried · 2 hydrogen bonds · protein-protein
- D–J · 325 Ų buried · 8 hydrogen bonds · protein-protein
- F–L · 322 Ų buried · 7 hydrogen bonds · protein-protein
- C–I · 315 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1XB1 · The Structure of the BIR domain of IAP-like protein 2 · the same entry in another collection · chain L against L, 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 Q96P09
- Every structure of UniProt Q9NR28
- Elsewhere: RCSB PDB 1XB1 · PDBe 1XB1 · UniProt Q96P09 · UniProt Q9NR28
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