Research workbench
Crystal structure of xiap BIR3 domain in complex with a smac-mimetic compound, SMAC010
Analyse Crystal structure of xiap BIR3 domain in complex with a smac-mimetic compound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CM2
- Type
- protein
- Length
- 1,024 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baculoviral iap repeat-containing protein 4
- EC
- 6.3.2.-
- UniProt
- P98170
- Ligands
- X23, ZN
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E, G, H, I | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 102 | 47% helix, 8% strand | P98170 |
| A, B, F | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 103 | 47% helix, 8% strand | P98170 |
| C | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 102 | 46% helix, 8% strand | P98170 |
| J | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 103 | 47% helix, 8% strand | P98170 |
Ligands and binding sites
- X23 · (3S,6S,7R,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-7-(aminomethyl)-N-(diphenylmethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide · ligand · 10 copies · chains D, H, A, B, C, G, E, I, F, J
- ZN · Zinc ion · metal · 10 copies · chains D, A, B, C, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.76 | 0.78 | 94 | X23 |
| 2 | 782 | 0.74 | 0.79 | 76 | X23 |
| 3 | 794 | 0.74 | 0.79 | 72 | X23 |
| 4 | 1079 | 0.74 | 0.77 | 109 | empty |
| 5 | 430 | 0.68 | 0.80 | 39 | X23 |
Interfaces
14 interfaces between chains.
- F–I · 902 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 863 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 851 Ų buried · 20 hydrogen bonds · protein-protein
- D–B · 828 Ų buried · 14 hydrogen bonds · protein-protein
- B–H · 547 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3CM2 · Crystal Structure of XIAP BIR3 domain in complex with a Smac-mimetic compound, Smac010 · the same entry in another collection · chain I against I, TM-score 1.00
- P98170 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase xiap (P98170) · a predicted model of the same protein · chain E against A, TM-score 0.95
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 P98170
- Elsewhere: RCSB PDB 3CM2 · PDBe 3CM2 · UniProt P98170
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