MolNFT v1 · #11828 · protein
The structure of human methemoglobin. the variation of a theme
1JY7 · Hemoglobin alpha chain: “The structure of human methemoglobin. the variation of a theme”. X-ray diffraction, 1 ligand (HEM), 20 pockets (best druggability 0.86). MolNFT v1 #11828 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1JY7
- Type
- protein
- Length
- 1,722 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha chain; Hemoglobin beta chain
- UniProt
- P69905, P68871
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, P, R, U, W | Hemoglobin alpha chain | protein | 141 | 74% helix, 0% strand | P69905 |
| B, D, Q, S, V, X | Hemoglobin beta chain | protein | 146 | 75% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, B, C, D, P, Q, R, S, U, V, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.86 | 0.86 | 92 | empty |
| 2 | 494 | 0.82 | 0.89 | 72 | empty |
| 3 | 578 | 0.81 | 0.87 | 60 | empty |
| 4 | 321 | 0.76 | 0.87 | 38 | HEM |
| 5 | 314 | 0.76 | 0.87 | 34 | HEM |
Interfaces
21 interfaces between chains.
- P–Q · 939 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 922 Ų buried · 10 hydrogen bonds · protein-protein
- U–V · 896 Ų buried · 10 hydrogen bonds · protein-protein
- W–X · 883 Ų buried · 12 hydrogen bonds · protein-protein
- R–S · 877 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1JY7 · The structure of human methemoglobin. the variation of a theme · 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 1JY7 · PDBe 1JY7 · UniProt P69905 · UniProt P68871
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