Research workbench
Crystal structure determination of cat (felis silvestris catus) hemoglobin at 2.9 ångström resolution
Analyse Crystal structure determination of cat (felis silvestris catus) hemoglobin at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GYS
- Type
- protein
- Length
- 1,133 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta-A/B
- UniProt
- P07405, P07412
- Ligands
- HEM
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G | Hemoglobin subunit alpha | protein | 138 | 79% helix, 0% strand | P07405 |
| B, D, F, H | Hemoglobin subunit beta-A/B | protein | 145 | 77% helix, 0% strand | P07412 |
| C | Hemoglobin subunit alpha | protein | 139 | 80% helix, 0% strand | P07405 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.83 | 0.84 | 102 | empty |
| 2 | 1146 | 0.83 | 0.84 | 114 | empty |
| 3 | 290 | 0.77 | 0.88 | 32 | HEM |
| 4 | 276 | 0.76 | 0.88 | 40 | HEM |
| 5 | 240 | 0.74 | 0.88 | 29 | HEM |
Interfaces
14 interfaces between chains.
- E–F · 910 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 861 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 850 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 844 Ų buried · 9 hydrogen bonds · protein-protein
- F–G · 498 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3GYS · Crystal structure determination of cat (Felis silvestris catus) hemoglobin at 2.9… · the same entry in another collection · chain E against E, TM-score 1.00
- P07405 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P07405) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P07412 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta-A/B (P07412) · 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 P07405
- Every structure of UniProt P07412
- Elsewhere: RCSB PDB 3GYS · PDBe 3GYS · UniProt P07405 · UniProt P07412
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.