Research workbench
The crystal structure of recombinant human adult hemoglobin
Analyse The crystal structure of recombinant human adult hemoglobin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KYE
- Type
- protein
- Length
- 1,716 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HEM, CMO
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, K | Hemoglobin subunit alpha | protein | 140 | 75% helix, 0% strand | P69905 |
| B, D, F, J, L | Hemoglobin subunit beta | protein | 146 | 75% helix, 0% strand | P68871 |
| H | Hemoglobin subunit beta | protein | 145 | 74% helix, 0% strand | P68871 |
| I | Hemoglobin subunit alpha | protein | 141 | 74% helix, 0% strand | P69905 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, F, B, C, D, E, G, H, I, J, K, L
- CMO · Carbon monoxide · ion · 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
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.83 | 0.89 | 68 | empty |
| 2 | 566 | 0.81 | 0.87 | 59 | empty |
| 3 | 610 | 0.81 | 0.86 | 48 | empty |
| 4 | 378 | 0.80 | 0.89 | 60 | empty |
| 5 | 184 | 0.75 | 0.90 | 24 | HEM, CMO |
Interfaces
22 interfaces between chains.
- K–L · 969 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 960 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 925 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 914 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 904 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6KYE · The crystal structure of recombinant human adult hemoglobin · the same entry in another collection · chain E against E, 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 6KYE · PDBe 6KYE · UniProt P69905 · UniProt P68871
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