MolNFT v1 · #151311 · protein
Crystal structure of ferric R-state human methemoglobin bound to maleimide-deferoxamine bifunctional chelator (dfo)
6HK2 · Hemoglobin subunit alpha: “Crystal structure of ferric R-state human methemoglobin bound to maleimide-deferoxamine bifunctional chelator…”. X-ray diffraction, 4 ligands (HEM, G7Z, SO4), 12 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 6HK2
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HEM, G7Z, SO4, OXY
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 82% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 146 | 82% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- G7Z · 3-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]-~{N}-methyl-propanamide · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, D, B, C
- OXY · Oxygen molecule · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.86 | 0.91 | 58 | SO4 |
| 2 | 381 | 0.79 | 0.89 | 46 | empty |
| 3 | 248 | 0.74 | 0.87 | 27 | HEM |
| 4 | 213 | 0.70 | 0.86 | 27 | HEM, OXY |
| 5 | 174 | 0.69 | 0.87 | 22 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 951 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 913 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 529 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 527 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 428 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6HK2 · Crystal structure of ferric R-state human methemoglobin bound to maleimide-deferoxamine… · 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 P69905
- Every structure of UniProt P68871
- Elsewhere: RCSB PDB 6HK2 · PDBe 6HK2 · UniProt P69905 · UniProt P68871
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