MolNFT v1 · #50090 · protein
Pigeon hemoglobin (oxy form)
2R80 · Hemoglobin subunit alpha-a: “Pigeon hemoglobin (oxy form)”. X-ray diffraction, 2 ligands (HEM, OXY), 8 pockets (best druggability 0.87). MolNFT v1 #50090 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2R80
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha-a; Hemoglobin subunit beta
- UniProt
- P21871, P11342
- Ligands
- HEM, OXY
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha-a | protein | 141 | 75% helix, 0% strand | P21871 |
| B, D | Hemoglobin subunit beta | protein | 146 | 79% helix, 0% strand | P11342 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.87 | 0.88 | 107 | empty |
| 2 | 253 | 0.74 | 0.87 | 33 | HEM, OXY |
| 3 | 222 | 0.74 | 0.88 | 31 | HEM, OXY |
| 4 | 246 | 0.73 | 0.87 | 28 | HEM, OXY |
| 5 | 217 | 0.73 | 0.88 | 30 | HEM, OXY |
Interfaces
6 interfaces between chains.
- C–D · 1004 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 977 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 501 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 485 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 350 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2R80 · Pigeon Hemoglobin (OXY form) · the same entry in another collection · chain C against C, TM-score 1.00
- P11342 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P11342) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P21871 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha-a (P21871) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P21871
- Every structure of UniProt P11342
- Elsewhere: RCSB PDB 2R80 · PDBe 2R80 · UniProt P21871 · UniProt P11342
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