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A triply ligated crystal structure of relaxed state human hemoglobin
Analyse A triply ligated crystal structure of relaxed state human hemoglobin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D17
- 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, MBN, CMO, PO4
- Pockets
- 10 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 81% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 146 | 75% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- MBN · Toluene · ligand · chains A
- CMO · Carbon monoxide · ion · 3 copies · chains A, B, D
- PO4 · Phosphate ion · ion · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.88 | 0.92 | 105 | CMO, HEM |
| 2 | 118 | 0.78 | 0.96 | 20 | MBN |
| 3 | 252 | 0.74 | 0.87 | 30 | HEM |
| 4 | 242 | 0.74 | 0.87 | 32 | CMO, HEM |
| 5 | 239 | 0.71 | 0.86 | 32 | CMO, HEM |
Interfaces
6 interfaces between chains.
- C–D · 872 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 869 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 555 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 543 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 413 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3D17 · A triply ligated crystal structure of relaxed state human hemoglobin · 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 3D17 · PDBe 3D17 · UniProt P69905 · UniProt P68871
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