MolNFT v1 · #70972 · protein
Crystal structure of the TRAF1:TRAF2:CIAP2 complex
3M0D · TNF receptor-associated factor 2: “Crystal structure of the TRAF1:TRAF2:CIAP2 complex”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.55). MolNFT v1 #70972 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3M0D
- Type
- protein
- Length
- 264 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TNF receptor-associated factor 2; TNF receptor-associated factor 1; Baculoviral iap…
- UniProt
- Q12933, Q13077, Q13489
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | TNF receptor-associated factor 2 | protein | 63 | 97% helix, 0% strand | Q12933 |
| C | TNF receptor-associated factor 1 | protein | 63 | 94% helix, 0% strand | Q13077 |
| D | Baculoviral iap repeat-containing protein 3 | protein | 75 | 37% helix, 11% strand | Q13489 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.55 | 0.90 | 19 | empty |
| 2 | 186 | 0.45 | 0.74 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1291 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 1237 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1180 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 498 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 271 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3M0D · Crystal structure of the TRAF1:TRAF2:cIAP2 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q13489 · AlphaFold monomer V2.0 prediction for baculoviral iap repeat- containing protein 3… · a predicted model of the same protein · chain D against A, TM-score 0.94
- Q12933 · AlphaFold monomer V2.0 prediction for TNF receptor-associated factor 2 (Q12933) · a predicted model of the same protein · chain A against A, TM-score 0.90
- Q13077 · AlphaFold monomer V2.0 prediction for TNF receptor-associated factor 1 (Q13077) · a predicted model of the same protein · chain C against A, TM-score 0.90
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 Q12933
- Every structure of UniProt Q13077
- Every structure of UniProt Q13489
- Elsewhere: RCSB PDB 3M0D · PDBe 3M0D · UniProt Q12933 · UniProt Q13077 · UniProt Q13489
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