MolNFT v1 · #65499 · protein
Crystal structure determination of cat (felis silvestris catus) hemoglobin at 2.9 ångström resolution
3GYS · Hemoglobin subunit alpha: “Crystal structure determination of cat (felis silvestris catus) hemoglobin at 2.9 ångström resolution”. X-ray diffraction, 1 ligand (HEM), 17 pockets (best druggability 0.83). MolNFT v1 #65499 on…
- 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
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