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The crystal structure of hpua from kingella denitrificans in complex with human haemoglobin
Analyse The crystal structure of hpua from kingella denitrificans in complex with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EE4
- Type
- protein
- Length
- 1,164 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hpua; Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- F0EX68, P69905, P68871
- Ligands
- HEM, OXY
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hpua | protein | 297 | 4% helix, 46% strand | F0EX68 |
| B | Hpua | protein | 298 | 4% helix, 47% strand | F0EX68 |
| C, E | Hemoglobin subunit alpha | protein | 141 | 76% helix, 0% strand | P69905 |
| D | Hemoglobin subunit beta | protein | 146 | 80% helix, 0% strand | P68871 |
| F | Hemoglobin subunit beta | protein | 141 | 79% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, D, E, F
- OXY · Oxygen molecule · ion · 4 copies · chains C, D, E, F
- GOL · Glycerol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.84 | 0.87 | 84 | empty |
| 2 | 1167 | 0.82 | 0.83 | 110 | empty |
| 3 | 981 | 0.81 | 0.83 | 95 | GOL |
| 4 | 247 | 0.73 | 0.86 | 29 | HEM, OXY |
| 5 | 248 | 0.72 | 0.86 | 27 | HEM, OXY |
Interfaces
10 interfaces between chains.
- A–D · 1027 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 919 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 912 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 891 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 474 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5EE4 · The crystal structure of HpuA from Kingella denitrificans in complex with human… · 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 F0EX68
- Every structure of UniProt P69905
- Every structure of UniProt P68871
- Elsewhere: RCSB PDB 5EE4 · PDBe 5EE4 · UniProt F0EX68 · UniProt P69905 · UniProt P68871
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