MolNFT v1 · #60654 · protein
Crystal structure determination of buffalo (bubalus bubalis) hemoglobin at 2 ångström resolution
3CY5 · Hemoglobin subunit alpha-2: “Crystal structure determination of buffalo (bubalus bubalis) hemoglobin at 2 ångström resolution”. X-ray diffraction, 1 ligand (HEM), 7 pockets (best druggability 0.86). MolNFT v1 #60654 on GenesisL1: 3D…
- PDB
- 3CY5
- Type
- protein
- Length
- 572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha-2; Hemoglobin subunit beta
- UniProt
- Q9TSN8, P67820
- Ligands
- HEM
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha-2 | protein | 141 | 75% helix, 0% strand | Q9TSN8 |
| B, D | Hemoglobin subunit beta | protein | 145 | 81% helix, 0% strand | P67820 |
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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.86 | 0.89 | 92 | empty |
| 2 | 224 | 0.73 | 0.88 | 30 | HEM |
| 3 | 267 | 0.72 | 0.85 | 39 | HEM |
| 4 | 187 | 0.71 | 0.87 | 24 | HEM |
| 5 | 185 | 0.69 | 0.86 | 22 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 907 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 876 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 622 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 562 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 277 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3CY5 · Crystal structure determination of buffalo (Bubalus bubalis) hemoglobin at 2 angstrom… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9TSN8 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha-2 (Q9TSN8) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P67820 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P67820) · 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 Q9TSN8
- Every structure of UniProt P67820
- Elsewhere: RCSB PDB 3CY5 · PDBe 3CY5 · UniProt Q9TSN8 · UniProt P67820
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