Research workbench
Human hemoglobin D los angeles: crystal structure
Analyse Human hemoglobin D los angeles: crystal structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YRS
- Type
- protein
- Length
- 1,148 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HEM
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, I, M | Hemoglobin subunit alpha | protein | 141 | 79% helix, 0% strand | P69905 |
| B, D, K, O | Hemoglobin subunit beta | protein | 146 | 75% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, I, K, M, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.82 | 0.84 | 86 | empty |
| 2 | 859 | 0.81 | 0.83 | 81 | empty |
| 3 | 234 | 0.74 | 0.87 | 30 | HEM |
| 4 | 213 | 0.73 | 0.88 | 29 | HEM |
| 5 | 199 | 0.71 | 0.87 | 29 | HEM |
Interfaces
12 interfaces between chains.
- C–D · 859 Ų buried · 11 hydrogen bonds · protein-protein
- M–O · 857 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 848 Ų buried · 12 hydrogen bonds · protein-protein
- I–K · 832 Ų buried · 9 hydrogen bonds · protein-protein
- I–O · 728 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2YRS · Human hemoglobin D Los Angeles: crystal structure · 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 2YRS · PDBe 2YRS · UniProt P69905 · UniProt P68871
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