Research workbench
CIAP1-BIR3 domain in complex with the smac-mimetic compound SMAC037
Analyse CIAP1-BIR3 domain in complex with the smac-mimetic compound SMAC037 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MUP
- Type
- protein
- Length
- 406 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baculoviral iap repeat-containing protein 2
- UniProt
- Q13490
- Ligands
- SMK, ZN
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Baculoviral iap repeat-containing protein 2 | protein | 101 | 49% helix, 8% strand | Q13490 |
| B | Baculoviral iap repeat-containing protein 2 | protein | 100 | 47% helix, 8% strand | Q13490 |
| C | Baculoviral iap repeat-containing protein 2 | protein | 103 | 47% helix, 8% strand | Q13490 |
| D | Baculoviral iap repeat-containing protein 2 | protein | 102 | 49% helix, 8% strand | Q13490 |
Ligands and binding sites
- SMK · (3S,6S,7R,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-7-(2-aminoethyl)-N-(diphenylmethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.56 | 0.77 | 34 | empty |
| 2 | 188 | 0.49 | 0.76 | 28 | empty |
| 3 | 141 | 0.41 | 0.74 | 27 | SMK |
| 4 | 91 | 0.40 | 0.77 | 22 | empty |
| 5 | 116 | 0.39 | 0.75 | 19 | SMK |
Interfaces
4 interfaces between chains.
- B–D · 475 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 423 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 409 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 404 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3MUP · cIAP1-BIR3 domain in complex with the Smac-mimetic compound Smac037 · the same entry in another collection · chain C against C, TM-score 1.00
- Q13490 · AlphaFold monomer V2.0 prediction for baculoviral iap repeat- containing protein 2… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q13490
- Elsewhere: RCSB PDB 3MUP · PDBe 3MUP · UniProt Q13490
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