MolNFT v1 · #74743 · protein
Ferric R-state human aquomethemoglobin
3P5Q · Hemoglobin subunit alpha: “Ferric R-state human aquomethemoglobin”. X-ray diffraction, 2 ligands (MBN, HEM), 5 pockets (best druggability 0.79). MolNFT v1 #74743 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3P5Q
- Type
- protein
- Length
- 285 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- MBN, HEM
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin subunit alpha | protein | 139 | 78% helix, 0% strand | P69905 |
| B | Hemoglobin subunit beta | protein | 146 | 77% helix, 0% strand | P68871 |
Ligands and binding sites
- MBN · Toluene · ligand · 3 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.79 | 0.96 | 23 | MBN |
| 2 | 201 | 0.73 | 0.88 | 25 | HEM |
| 3 | 176 | 0.68 | 0.86 | 24 | HEM |
| 4 | 109 | 0.49 | 0.81 | 20 | empty |
| 5 | 71 | 0.38 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 928 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3P5Q · Ferric R-state human aquomethemoglobin · 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 3P5Q · PDBe 3P5Q · UniProt P69905 · UniProt P68871
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