Research workbench
Structural basis for the heterotropic and homotropic interactions of invertebrate giant hemoglobin
Analyse Structural basis for the heterotropic and homotropic interactions of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZS0
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular giant hemoglobin major globin subunit A1; Extracellular giant hemoglobin…
- UniProt
- Q7M419, Q7M413, Q7M418, Q5KSB7
- Ligands
- HEM, CA, OXY, CL
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular giant hemoglobin major globin subunit A1 | protein | 140 | 81% helix, 0% strand | Q7M419 |
| B | Extracellular giant hemoglobin major globin subunit A2 | protein | 142 | 77% helix, 0% strand | Q7M413 |
| C | Extracellular giant hemoglobin major globin subunit B2 | protein | 147 | 74% helix, 0% strand | Q7M418 |
| D | Extracellular giant hemoglobin major globin subunit B1 | protein | 145 | 72% helix, 0% strand | Q5KSB7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, D, B, C
- CA · Calcium ion · metal · 4 copies · chains A, B, C
- OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A, C
- GOL · Glycerol · additive · 2 copies · chains C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.85 | 0.86 | 68 | HEM, OXY |
| 2 | 715 | 0.83 | 0.86 | 65 | HEM, OXY |
| 3 | 676 | 0.75 | 0.81 | 80 | CL, CA |
| 4 | 60 | 0.41 | 0.81 | 15 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1197 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 815 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 537 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 526 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 154 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2ZS0 · Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant… · the same entry in another collection · chain D against D, TM-score 1.00
- Q7M419 · AlphaFold monomer V2.0 prediction for extracellular giant hemoglobin major globin subunit… · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q7M413 · AlphaFold monomer V2.0 prediction for extracellular giant hemoglobin major globin subunit… · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q5KSB7 · AlphaFold monomer V2.0 prediction for extracellular giant hemoglobin major globin subunit… · a predicted model of the same protein · chain D against A, TM-score 0.96
- Q7M418 · AlphaFold monomer V2.0 prediction for extracellular giant hemoglobin major globin subunit… · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q7M419
- Every structure of UniProt Q7M413
- Every structure of UniProt Q7M418
- Every structure of UniProt Q5KSB7
- Elsewhere: RCSB PDB 2ZS0 · PDBe 2ZS0 · UniProt Q7M419 · UniProt Q7M413 · UniProt Q7M418 · UniProt Q5KSB7
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