MolNFT v1 · #56165 · protein
Crystal structure of carbonmonoxy hemoglobin D from the aldabra giant tortoise, geochelone gigantea
2Z6N · Hemoglobin D subunit alpha: “Crystal structure of carbonmonoxy hemoglobin D from the aldabra giant tortoise, geochelone gigantea”. X-ray diffraction, 2 ligands (HEM, CMO), 3 pockets (best druggability 0.73). MolNFT v1 #56165 on…
- PDB
- 2Z6N
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin D subunit alpha; Hemoglobin A/D subunit beta
- UniProt
- P83134, P83133
- Ligands
- HEM, CMO
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin D subunit alpha | protein | 141 | 84% helix, 0% strand | P83134 |
| B | Hemoglobin A/D subunit beta | protein | 146 | 77% helix, 0% strand | P83133 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CMO · Carbon monoxide · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.73 | 0.87 | 28 | HEM, CMO |
| 2 | 181 | 0.69 | 0.87 | 25 | HEM, CMO |
| 3 | 136 | 0.49 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 887 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2Z6N · Crystal Structure of Carbonmonoxy Hemoglobin D from the Aldabra Giant Tortoise… · the same entry in another collection · chain A against A, TM-score 1.00
- P83133 · AlphaFold monomer V2.0 prediction for hemoglobin A/D subunit beta (P83133) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P83134 · AlphaFold monomer V2.0 prediction for hemoglobin D subunit alpha (P83134) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P83134
- Every structure of UniProt P83133
- Elsewhere: RCSB PDB 2Z6N · PDBe 2Z6N · UniProt P83134 · UniProt P83133
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