Research workbench
Crystal structure determination of shortfin mako (isurus oxyrinchus) hemoglobin at 1.9 ångström resolution
Analyse Crystal structure determination of shortfin mako (isurus oxyrinchus) hemoglobin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MKB
- Type
- protein
- Length
- 544 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- Ligands
- HEM
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 140 | 74% helix, 0% strand | — |
| B | Hemoglobin subunit beta | protein | 133 | 79% helix, 0% strand | — |
| D | Hemoglobin subunit beta | protein | 131 | 78% helix, 0% strand | — |
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
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.78 | 0.80 | 84 | empty |
| 2 | 185 | 0.71 | 0.88 | 26 | HEM |
| 3 | 211 | 0.71 | 0.87 | 26 | HEM |
| 4 | 206 | 0.69 | 0.86 | 35 | HEM |
| 5 | 189 | 0.67 | 0.85 | 29 | HEM |
Interfaces
5 interfaces between chains.
- C–D · 775 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 768 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 543 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 543 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 294 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3MKB · Crystal structure determination of Shortfin Mako (Isurus oxyrinchus) hemoglobin at 1.9… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3MKB · PDBe 3MKB
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