Research workbench
Crystal structure of HID2 bound to human hemoglobin
Analyse Crystal structure of HID2 bound to human hemoglobin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CUE
- Type
- protein
- Length
- 898 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta; Amino acid ABC transporter…
- UniProt
- P69905, P68871, B0LFQ8
- Ligands
- HEM, SO4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 74% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 146 | 79% helix, 0% strand | P68871 |
| E, F, H | Amino acid ABC transporter substrate-binding protein | protein | 108 | 7% helix, 46% strand | B0LFQ8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, E, B, F, C, D, H
- SO4 · Sulfate ion · ion · 2 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.83 | 0.84 | 111 | HEM |
| 2 | 590 | 0.82 | 0.87 | 53 | empty |
| 3 | 558 | 0.80 | 0.86 | 55 | empty |
| 4 | 597 | 0.75 | 0.81 | 60 | HEM, SO4 |
| 5 | 233 | 0.72 | 0.87 | 28 | HEM |
Interfaces
10 interfaces between chains.
- A–B · 933 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 924 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 542 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 529 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 510 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7CUE · Crystal structure of HID2 bound to human Hemoglobin · the same entry in another collection · chain H against H, TM-score 1.00
- P68871 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P68871) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P69905 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P69905) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P69905
- Every structure of UniProt P68871
- Every structure of UniProt B0LFQ8
- Elsewhere: RCSB PDB 7CUE · PDBe 7CUE · UniProt P69905 · UniProt P68871 · UniProt B0LFQ8
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