MolNFT v1 · #120135 · protein
Structure of alg-2/HEBP2 complex
5GQQ · Heme-binding protein 2: “Structure of alg-2/HEBP2 complex”. X-ray diffraction, 2 ligands (CA, CL), 4 pockets (best druggability 0.87). MolNFT v1 #120135 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GQQ
- Type
- protein
- Length
- 693 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heme-binding protein 2; Programmed cell death protein 6
- UniProt
- Q9Y5Z4, O75340
- Ligands
- CA, CL
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Heme-binding protein 2 | protein | 178 | 21% helix, 35% strand | Q9Y5Z4 |
| C | Programmed cell death protein 6 | protein | 170 | 57% helix, 6% strand | O75340 |
| D | Programmed cell death protein 6 | protein | 167 | 59% helix, 7% strand | O75340 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains B, C, A, D
- CL · Chloride ion · ion · 2 copies · chains B, C, A, D
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 | 1160 | 0.87 | 0.88 | 130 | empty |
| 2 | 157 | 0.55 | 0.81 | 28 | empty |
| 3 | 167 | 0.53 | 0.79 | 26 | empty |
| 4 | 51 | 0.41 | 0.82 | 14 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1672 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 980 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 936 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 352 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 350 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5GQQ · Structure of ALG-2/HEBP2 Complex · the same entry in another collection · chain A against A, TM-score 1.00
- O75340 · AlphaFold monomer V2.0 prediction for programmed cell death protein 6 (O75340) · a predicted model of the same protein · chain D against A, TM-score 0.96
- Q9Y5Z4 · AlphaFold monomer V2.0 prediction for heme-binding protein 2 (Q9Y5Z4) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9Y5Z4
- Every structure of UniProt O75340
- Elsewhere: RCSB PDB 5GQQ · PDBe 5GQQ · UniProt Q9Y5Z4 · UniProt O75340
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