Research workbench
Crystal structure analysis of bar-head goose hemoglobin (deoxy form)
Analyse Crystal structure analysis of bar-head goose hemoglobin (deoxy form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HV4
- Type
- protein
- Length
- 1,148 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha-a chain; Hemoglobin beta chain
- UniProt
- P01990, P02118
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Hemoglobin alpha-a chain | protein | 141 | 77% helix, 0% strand | P01990 |
| B, D, F, H | Hemoglobin beta chain | protein | 146 | 81% helix, 0% strand | P02118 |
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
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.87 | 0.88 | 78 | HEM |
| 2 | 854 | 0.86 | 0.88 | 80 | HEM |
| 3 | 1091 | 0.83 | 0.84 | 79 | empty |
| 4 | 622 | 0.81 | 0.86 | 44 | empty |
| 5 | 201 | 0.76 | 0.90 | 25 | HEM |
Interfaces
14 interfaces between chains.
- E–F · 972 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 969 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 969 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 965 Ų buried · 8 hydrogen bonds · protein-protein
- E–H · 486 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1HV4 · Crystal structure analysis of bar-head goose hemoglobin (deoxy form) · the same entry in another collection · chain H against H, TM-score 1.00
- P02118 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P02118) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P01990 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha-a (P01990) · 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 P01990
- Every structure of UniProt P02118
- Elsewhere: RCSB PDB 1HV4 · PDBe 1HV4 · UniProt P01990 · UniProt P02118
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