Research workbench
Crystal structure determination of goat hemoglobin at 2.61 ångström resolution
Analyse Crystal structure determination of goat hemoglobin at 2.61 ångström resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D1A
- Type
- protein
- Length
- 572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha-1/2; Hemoglobin subunit beta-a
- UniProt
- P68238, P02077
- Ligands
- HEM
- Pockets
- 5 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha-1/2 | protein | 141 | 74% helix, 0% strand | P68238 |
| B, D | Hemoglobin subunit beta-a | protein | 145 | 81% helix, 0% strand | P02077 |
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
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.88 | 0.90 | 102 | empty |
| 2 | 233 | 0.74 | 0.88 | 28 | HEM |
| 3 | 255 | 0.74 | 0.87 | 30 | HEM |
| 4 | 218 | 0.72 | 0.87 | 29 | HEM |
| 5 | 200 | 0.70 | 0.86 | 26 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 891 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 872 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 566 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 514 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 281 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3D1A · Crystal Structure Determination of Goat Hemoglobin at 2.61 Angstrom Resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P02077 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta-a (P02077) · 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 P68238
- Every structure of UniProt P02077
- Elsewhere: RCSB PDB 3D1A · PDBe 3D1A · UniProt P68238 · UniProt P02077
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