Research workbench
Graylag goose hemoglobin (oxy form)
Analyse Graylag goose hemoglobin (oxy form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FAW
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin (alpha subunit); Hemoglobin (beta subunit)
- UniProt
- P01989, P02117
- Ligands
- HEM, OXY
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin (alpha subunit) | protein | 141 | 77% helix, 0% strand | P01989 |
| B, D | Hemoglobin (beta subunit) | protein | 146 | 80% helix, 0% strand | P02117 |
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
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 | 1115 | 0.87 | 0.88 | 107 | empty |
| 2 | 255 | 0.74 | 0.87 | 26 | HEM, OXY |
| 3 | 280 | 0.73 | 0.85 | 31 | HEM, OXY |
| 4 | 225 | 0.70 | 0.86 | 24 | HEM, OXY |
| 5 | 216 | 0.69 | 0.85 | 24 | HEM, OXY |
Interfaces
6 interfaces between chains.
- A–B · 962 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 957 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 480 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 471 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 342 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1FAW · Graylag goose hemoglobin (oxy form) · the same entry in another collection · chain D against D, TM-score 1.00
- P02117 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P02117) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P01989 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha-a (P01989) · a predicted model of the same protein · chain A 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 P01989
- Every structure of UniProt P02117
- Elsewhere: RCSB PDB 1FAW · PDBe 1FAW · UniProt P01989 · UniProt P02117
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