Research workbench
Deoxy form hemoglobin from mustelus griseus
Analyse Deoxy form hemoglobin from mustelus griseus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GCV
- Type
- protein
- Length
- 552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Mustelus griseus
- Molecule
- Hemoglobin
- UniProt
- Q9YGW2, Q9YGW1
- Ligands
- HEM
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin | protein | 140 | 79% helix, 0% strand | Q9YGW2 |
| B, D | Hemoglobin | protein | 136 | 79% helix, 0% strand | Q9YGW1 |
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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.79 | 0.81 | 78 | empty |
| 2 | 256 | 0.74 | 0.87 | 26 | HEM |
| 3 | 282 | 0.72 | 0.85 | 29 | HEM |
| 4 | 288 | 0.72 | 0.85 | 31 | HEM |
| 5 | 236 | 0.71 | 0.86 | 26 | HEM |
Interfaces
5 interfaces between chains.
- C–D · 827 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 826 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 678 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 650 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 317 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1GCV · Deoxy form hemoglobin from mustelus griseus · the same entry in another collection · chain A against A, TM-score 1.00
- Q9YGW1 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (Q9YGW1) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q9YGW2 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (Q9YGW2) · 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 Q9YGW2
- Every structure of UniProt Q9YGW1
- Elsewhere: RCSB PDB 1GCV · PDBe 1GCV · UniProt Q9YGW2 · UniProt Q9YGW1
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