Research workbench
Crystal structure of hemoglobin from turkey (meleagiris gallopova) crystallized in orthorhombic form at 1.4 ångström resolution
Analyse Crystal structure of hemoglobin from turkey (meleagiris gallopova) crystallized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZMX
- Type
- protein
- Length
- 568 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, NA
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha-a | protein | 138 | 75% helix, 0% strand | P81023 |
| B, D | Hemoglobin beta chain | protein | 146 | 80% helix, 0% strand | P84479 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.84 | 0.88 | 78 | HEM |
| 2 | 714 | 0.84 | 0.87 | 70 | empty |
| 3 | 241 | 0.75 | 0.88 | 31 | HEM |
| 4 | 201 | 0.73 | 0.88 | 32 | HEM |
| 5 | 202 | 0.69 | 0.86 | 24 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 1019 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1011 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 394 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 392 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 321 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6ZMX · Crystal structure of hemoglobin from turkey (Meleagiris gallopova) crystallized in… · 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 0.99
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 6ZMX · PDBe 6ZMX · UniProt P81023 · UniProt P84479
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