Research workbench
T. congolense haptoglobin-haemoglobin receptor in complex with haemoglobin
Analyse T. congolense haptoglobin-haemoglobin receptor in complex with haemoglobin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JDO
- Type
- protein
- Length
- 1,064 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haptoglobin-haemoglobin receptor; Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- G0UVW6, P69905, P68871
- Ligands
- HEM, OXY
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Haptoglobin-haemoglobin receptor | protein | 249 | 79% helix, 0% strand | G0UVW6 |
| B | Haptoglobin-haemoglobin receptor | protein | 245 | 83% helix, 0% strand | G0UVW6 |
| C | Hemoglobin subunit alpha | protein | 141 | 77% helix, 0% strand | P69905 |
| D | Hemoglobin subunit beta | protein | 145 | 77% helix, 0% strand | P68871 |
| E | Hemoglobin subunit alpha | protein | 140 | 77% helix, 0% strand | P69905 |
| F | Hemoglobin subunit beta | protein | 144 | 78% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains B, C, A, D, E, F
- OXY · Oxygen molecule · ion · 4 copies · chains C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.82 | 0.83 | 99 | empty |
| 2 | 571 | 0.80 | 0.85 | 45 | HEM, OXY |
| 3 | 509 | 0.79 | 0.86 | 54 | HEM, OXY |
| 4 | 563 | 0.79 | 0.85 | 55 | HEM, OXY |
| 5 | 759 | 0.79 | 0.82 | 63 | HEM, OXY |
Interfaces
10 interfaces between chains.
- C–D · 917 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 912 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 643 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 641 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 569 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5JDO · T. congolense haptoglobin-haemoglobin receptor in complex with haemoglobin · the same entry in another collection · chain A against A, TM-score 1.00
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 G0UVW6
- Every structure of UniProt P69905
- Every structure of UniProt P68871
- Elsewhere: RCSB PDB 5JDO · PDBe 5JDO · UniProt G0UVW6 · UniProt P69905 · UniProt P68871
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