Research workbench
Crystal structure of CIAP1 ring domain bound to UBCH5B-ub and a non- covalent ub
Analyse Crystal structure of CIAP1 ring domain bound to UBCH5B-ub and a non- covalent ub in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HPR
- Type
- protein
- Length
- 364 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baculoviral iap repeat-containing protein 2; Polyubiquitin-B; Ubiquitin-conjugating…
- EC
- 2.3.2.27, 2.3.2.23, 2.3.2.24
- UniProt
- Q13490, P0CG47, P62837
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Baculoviral iap repeat-containing protein 2 (EC 2.3.2.27) | protein | 63 | 22% helix, 24% strand | Q13490 |
| B | Polyubiquitin-B | protein | 77 | 23% helix, 36% strand | P0CG47 |
| C | Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24) | protein | 146 | 36% helix, 22% strand | P62837 |
| D | Polyubiquitin-B | protein | 78 | 23% helix, 36% strand | P0CG47 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.68 | 0.80 | 44 | empty |
| 2 | 306 | 0.59 | 0.77 | 47 | empty |
| 3 | 117 | 0.48 | 0.80 | 23 | empty |
| 4 | 79 | 0.34 | 0.75 | 18 | empty |
Interfaces
4 interfaces between chains.
- C–D · 939 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 754 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 517 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 338 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 6HPR · Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub · the same entry in another collection · chain A against A, TM-score 1.00
- P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain C against A, TM-score 0.98
- 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 0.76
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
- Every structure of UniProt P0CG47
- Every structure of UniProt P62837
- Elsewhere: RCSB PDB 6HPR · PDBe 6HPR · UniProt Q13490 · UniProt P0CG47 · UniProt P62837
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