Research workbench
Crystal structure of emu (dromaius novaehollandiae) hemoglobin at 2.3 ångström resolution
Analyse Crystal structure of emu (dromaius novaehollandiae) hemoglobin at 2.3 ångström… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WTG
- Type
- protein
- Length
- 568 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha-a; Hemoglobin
- UniProt
- C6L8R0
- Ligands
- HEM, OXY
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha-a | protein | 138 | 77% helix, 0% strand | C6L8R0 |
| B, D | Hemoglobin | protein | 146 | 82% helix, 0% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.82 | 0.89 | 50 | empty |
| 2 | 289 | 0.80 | 0.90 | 48 | HEM, OXY |
| 3 | 218 | 0.78 | 0.91 | 41 | HEM, OXY |
| 4 | 199 | 0.68 | 0.85 | 24 | HEM, OXY |
| 5 | 210 | 0.68 | 0.85 | 28 | HEM, OXY |
Interfaces
6 interfaces between chains.
- C–D · 1024 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1008 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 471 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 433 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 348 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3WTG · Crystal structure of Emu (dromaius novaehollandiae) hemoglobin at 2.3 angstrom resolution · 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 C6L8R0
- Elsewhere: RCSB PDB 3WTG · PDBe 3WTG · UniProt C6L8R0
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