Research workbench
Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 13% oxygen saturation
Analyse Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 13% oxygen saturation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E99
- Type
- protein
- Length
- 573 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Oligobrachia mashikoi
- Molecule
- Extracellular giant hemoglobin major globin subunit A1; Extracellular giant hemoglobin…
- UniProt
- Q7M419, Q7M413, Q7M418, B1Q3G1
- Ligands
- HEM, OXY
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.1 · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular giant hemoglobin major globin subunit A1 | protein | 140 | 78% helix, 0% strand | Q7M419 |
| B | Extracellular giant hemoglobin major globin subunit A2 | protein | 142 | 75% helix, 0% strand | Q7M413 |
| C | Extracellular giant hemoglobin major globin subunit B2 | protein | 146 | 74% helix, 0% strand | Q7M418 |
| D | Giant hemoglobin B1b globin chain | protein | 145 | 71% helix, 0% strand | B1Q3G1 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, D, B, C
- 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
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.83 | 0.85 | 66 | HEM, OXY |
| 2 | 664 | 0.81 | 0.85 | 63 | HEM, OXY |
| 3 | 247 | 0.61 | 0.80 | 53 | empty |
| 4 | 95 | 0.58 | 0.87 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1219 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1209 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 574 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 415 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 156 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7E99 · Oxy-deoxy intermediate of 400 kda giant hemoglobin at 13% oxygen saturation · the same entry in another collection · 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
- 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 0.98
- 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 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 Q7M419
- Every structure of UniProt Q7M413
- Every structure of UniProt Q7M418
- Every structure of UniProt B1Q3G1
- Elsewhere: RCSB PDB 7E99 · PDBe 7E99 · UniProt Q7M419 · UniProt Q7M413 · UniProt Q7M418 · UniProt B1Q3G1
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