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The 2.7 ångström crystal structure of deoxygenated hemoglobin from the sea lamprey (petromyzon marinus)
Analyse The 2.7 ångström crystal structure of deoxygenated hemoglobin from the sea… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LHB
- Type
- protein
- Length
- 1,788 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (hemoglobin)
- UniProt
- P02208
- Ligands
- HEM
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Protein (hemoglobin) | protein | 149 | 77% helix, 0% strand | P02208 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.85 | 0.88 | 86 | HEM |
| 2 | 669 | 0.85 | 0.88 | 61 | HEM |
| 3 | 812 | 0.83 | 0.85 | 84 | HEM |
| 4 | 1031 | 0.81 | 0.82 | 86 | HEM |
| 5 | 317 | 0.79 | 0.89 | 45 | HEM |
Interfaces
20 interfaces between chains.
- E–F · 506 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 506 Ų buried · 14 hydrogen bonds · protein-protein
- I–J · 506 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 502 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 502 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3LHB · The 2.7 ångström crystal structure of deoxygenated hemoglobin from the sea lamprey… · the same entry in another collection · chain L against L, 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
- Every structure of UniProt P02208
- Elsewhere: RCSB PDB 3LHB · PDBe 3LHB · UniProt P02208
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