Research workbench
2.9 ångström crystal structure of deoxygenated lamprey hemoglobin V in the space group P2(1)2(1)2(1)
Analyse 2.9 ångström crystal structure of deoxygenated lamprey hemoglobin V in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F5O
- Type
- protein
- Length
- 894 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin V
- UniProt
- P02208
- Ligands
- HEM
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Hemoglobin V | protein | 149 | 75% helix, 0% strand | P02208 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
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 | 1064 | 0.81 | 0.82 | 85 | HEM |
| 2 | 1043 | 0.81 | 0.82 | 87 | HEM |
| 3 | 1063 | 0.81 | 0.82 | 89 | HEM |
| 4 | 50 | 0.26 | 0.74 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 525 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 510 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 506 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1F5O · 2.9 ångström crystal structure of deoxygenated lamprey hemoglobin V in the space group… · the same entry in another collection · chain F against F, TM-score 1.00
- P02208 · AlphaFold monomer V2.0 prediction for globin-5 (P02208) · a predicted model of the same protein · chain F 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
- Every structure of UniProt P02208
- Elsewhere: RCSB PDB 1F5O · PDBe 1F5O · UniProt P02208
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