Research workbench
Crystal structure of turkey (meleagiris GALLOPOVA)HEMOGLOBIN at 2.3 ångström
Analyse Crystal structure of turkey (meleagiris GALLOPOVA)HEMOGLOBIN at 2.3 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K8B
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha-a; Hemoglobin beta chain
- UniProt
- P81023, P84479
- Ligands
- HEM
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha-a | protein | 141 | 72% helix, 0% strand | P81023 |
| B, D | Hemoglobin beta chain | protein | 146 | 79% helix, 0% strand | P84479 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.82 | 0.90 | 54 | empty |
| 2 | 353 | 0.79 | 0.89 | 63 | empty |
| 3 | 240 | 0.74 | 0.87 | 28 | HEM |
| 4 | 231 | 0.72 | 0.86 | 28 | HEM |
| 5 | 196 | 0.71 | 0.87 | 25 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 985 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 951 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 478 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 471 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 270 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3K8B · Crystal structure of Turkey (Meleagiris gallopova)hemoglobin at 2.3 Angstrom · the same entry in another collection · chain A against A, TM-score 1.00
- P81023 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha-a (P81023) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P81023
- Every structure of UniProt P84479
- Elsewhere: RCSB PDB 3K8B · PDBe 3K8B · UniProt P81023 · UniProt P84479
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