Research workbench
Cryoem structure of haemoglobin at 3.2 a determined with the volta phase plate
Analyse Cryoem structure of haemoglobin at 3.2 a determined with the volta phase plate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NI1
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HEM
- Pockets
- 8 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 74% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 146 | 78% helix, 0% strand | P68871 |
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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.83 | 0.84 | 114 | empty |
| 2 | 622 | 0.77 | 0.83 | 68 | empty |
| 3 | 262 | 0.73 | 0.86 | 28 | HEM |
| 4 | 258 | 0.71 | 0.85 | 28 | HEM |
| 5 | 243 | 0.71 | 0.85 | 25 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 939 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 932 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 445 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 441 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 348 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5NI1 · CryoEM structure of haemoglobin at 3.2 A determined with the Volta phase plate · 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
- Every structure of UniProt P69905
- Every structure of UniProt P68871
- Elsewhere: RCSB PDB 5NI1 · PDBe 5NI1 · UniProt P69905 · UniProt P68871
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