Research workbench
Crystal structure of pa-tm-ring E3 ligase RNF13 ring domain in complex with E2~UB
Analyse Crystal structure of pa-tm-ring E3 ligase RNF13 ring domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZBU
- Type
- protein
- Length
- 517 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D2; E3 ubiquitin-protein ligase RNF13; Ubiquitin
- EC
- 2.3.2.23, 2.3.2.24, 2.3.2.27
- UniProt
- P62837, O43567, P0CG47
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24) | protein | 148 | 38% helix, 17% strand | P62837 |
| B | Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24) | protein | 147 | 38% helix, 18% strand | P62837 |
| A | E3 ubiquitin-protein ligase RNF13 (EC 2.3.2.27) | protein | 74 | 19% helix, 19% strand | O43567 |
| D | E3 ubiquitin-protein ligase RNF13 (EC 2.3.2.27) | protein | 72 | 22% helix, 19% strand | O43567 |
| E | Ubiquitin | protein | 76 | 24% helix, 34% strand | P0CG47 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.71 | 0.75 | 64 | empty |
| 2 | 217 | 0.51 | 0.76 | 35 | empty |
Interfaces
7 interfaces between chains.
- C–D · 598 Ų buried · 4 hydrogen bonds · protein-protein
- B–A · 589 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 412 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 257 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 103 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 5ZBU · Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub · the same entry in another collection · chain E against E, TM-score 1.00
- O43567 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF13 (O43567) · a predicted model of the same protein · chain D against A, TM-score 0.98
- 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 0.97
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 P62837
- Every structure of UniProt O43567
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5ZBU · PDBe 5ZBU · UniProt P62837 · UniProt O43567 · UniProt P0CG47
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