Research workbench
2.9 ångström crystal structure of lamprey hemoglobin that has been exposed to carbon monoxide.
Analyse 2.9 ångström crystal structure of lamprey hemoglobin that has been exposed to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F5P
- 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, CMO
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Hemoglobin V | protein | 149 | 74% helix, 0% strand | P02208 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
- CMO · Carbon monoxide · ion · 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 | 1050 | 0.81 | 0.82 | 82 | HEM, CMO |
| 2 | 1094 | 0.81 | 0.82 | 87 | HEM, CMO |
| 3 | 1119 | 0.80 | 0.81 | 88 | HEM, CMO |
| 4 | 50 | 0.28 | 0.75 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 529 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 516 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 514 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 36 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1F5P · 2.9 ångström crystal structure of lamprey hemoglobin that has been exposed to carbon… · 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 E 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 1F5P · PDBe 1F5P · UniProt P02208
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