MolNFT v1 · #7653 · protein
Co form hemoglobin from mustelus griseus
1GCW · Protein (hemoglobin): “Co form hemoglobin from mustelus griseus”. X-ray diffraction, 2 ligands (HEM, CMO), 6 pockets (best druggability 0.81). MolNFT v1 #7653 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1GCW
- Type
- protein
- Length
- 538 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (hemoglobin)
- UniProt
- Q9YGW2, Q9YGW1
- Ligands
- HEM, CMO
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein (hemoglobin) | protein | 140 | 74% helix, 0% strand | Q9YGW2 |
| B, D | Protein (hemoglobin) | protein | 129 | 83% helix, 0% strand | Q9YGW1 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- CMO · Carbon monoxide · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.81 | 0.83 | 85 | empty |
| 2 | 247 | 0.74 | 0.87 | 26 | HEM, CMO |
| 3 | 240 | 0.74 | 0.87 | 25 | HEM, CMO |
| 4 | 249 | 0.72 | 0.86 | 27 | HEM, CMO |
| 5 | 252 | 0.71 | 0.85 | 26 | HEM, CMO |
Interfaces
6 interfaces between chains.
- C–D · 854 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 846 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 535 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 512 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 284 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1GCW · CO form hemoglobin from mustelus griseus · the same entry in another collection · chain A against A, TM-score 1.00
- 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
- Q9YGW1 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (Q9YGW1) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9YGW2
- Every structure of UniProt Q9YGW1
- Elsewhere: RCSB PDB 1GCW · PDBe 1GCW · UniProt Q9YGW2 · UniProt Q9YGW1
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