MolNFT v1 · #152877 · protein
Crystal structure of a computationally designed protein (LD3) in complex with BCL-2
6IWB · Apolipoprotein E: “Crystal structure of a computationally designed protein (LD3) in complex with BCL-2”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.66). MolNFT v1 #152877 on GenesisL1: 3D structure, binding…
- PDB
- 6IWB
- Type
- protein
- Length
- 563 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apolipoprotein E; Apoptosis regulator BCL-2,APOPTOSIS regulator BCL-2
- UniProt
- P02649, P10415
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apolipoprotein E | protein | 142 | 81% helix, 0% strand | P02649 |
| B, D | Apoptosis regulator BCL-2,APOPTOSIS regulator BCL-2 | protein | 139 | 69% helix, 0% strand | P10415 |
| C | Apolipoprotein E | protein | 143 | 79% helix, 0% strand | P02649 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.66 | 0.84 | 46 | SO4 |
| 2 | 65 | 0.56 | 0.88 | 16 | empty |
| 3 | 153 | 0.48 | 0.77 | 20 | empty |
| 4 | 167 | 0.47 | 0.76 | 24 | empty |
| 5 | 125 | 0.40 | 0.75 | 22 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1329 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1286 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 571 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 568 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 53 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6IWB · Crystal structure of a computationally designed protein (LD3) in complex with BCL-2 · the same entry in another collection · chain D against D, TM-score 1.00
- P02649 · AlphaFold monomer V2.0 prediction for apolipoprotein E (P02649) · a predicted model of the same protein · chain A against A, TM-score 0.94
- P10415 · AlphaFold monomer V2.0 prediction for apoptosis regulator BCL-2 (P10415) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 P02649
- Every structure of UniProt P10415
- Elsewhere: RCSB PDB 6IWB · PDBe 6IWB · UniProt P02649 · UniProt P10415
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