MolNFT v1 · #128982 · protein
BIRC4 ring in complex with dimeric ubiquitin variant
5O6T · E3 ubiquitin-protein ligase xiap: “BIRC4 ring in complex with dimeric ubiquitin variant”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.60). MolNFT v1 #128982 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5O6T
- Type
- protein
- Length
- 276 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase xiap; Polyubiquitin-B
- EC
- 2.3.2.27
- UniProt
- P98170, P0CG47
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase xiap (EC 2.3.2.27) | protein | 64 | 23% helix, 23% strand | P98170 |
| B | E3 ubiquitin-protein ligase xiap (EC 2.3.2.27) | protein | 63 | 24% helix, 27% strand | P98170 |
| C | Polyubiquitin-B | protein | 75 | 24% helix, 39% strand | P0CG47 |
| D | Polyubiquitin-B | protein | 74 | 24% helix, 39% strand | P0CG47 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.60 | 0.84 | 20 | empty |
| 2 | 194 | 0.60 | 0.81 | 30 | empty |
| 3 | 215 | 0.58 | 0.80 | 40 | empty |
| 4 | 205 | 0.49 | 0.76 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1966 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 1072 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 325 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 317 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 246 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5O6T · BIRC4 RING in complex with dimeric ubiquitin variant · 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 P98170
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5O6T · PDBe 5O6T · UniProt P98170 · UniProt P0CG47
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