Research workbench
Hemoglobin dodecamer from lumbricus erythrocruorin
Analyse Hemoglobin dodecamer from lumbricus erythrocruorin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X9F
- Type
- protein
- Length
- 1,743 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Globin IV, extracellular; Globin II, extracellular; Globin III, extracellular; Hemoglobin…
- UniProt
- P13579, P02218, P11069, O61233
- Ligands
- HEM, CMO, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Globin IV, extracellular | protein | 147 | 71% helix, 0% strand | P13579 |
| B, F, J | Globin II, extracellular | protein | 145 | 77% helix, 0% strand | P02218 |
| C, G, K | Globin III, extracellular | protein | 149 | 76% helix, 0% strand | P11069 |
| D, H, L | Hemoglobin chain D1 | protein | 140 | 82% helix, 0% strand | O61233 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, D, B, C, E, H, F, G, I, L, J, K
- CMO · Carbon monoxide · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- PO4 · Phosphate ion · ion · 3 copies · chains B, C, F, G, J, K
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 | 949 | 0.85 | 0.86 | 67 | HEM, CMO |
| 2 | 894 | 0.84 | 0.86 | 66 | HEM, CMO |
| 3 | 875 | 0.84 | 0.86 | 68 | HEM, CMO |
| 4 | 838 | 0.84 | 0.86 | 71 | HEM, CMO |
| 5 | 861 | 0.84 | 0.85 | 68 | HEM, CMO |
Interfaces
24 interfaces between chains.
- I–L · 1233 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1209 Ų buried · 17 hydrogen bonds · protein-protein
- E–H · 1198 Ų buried · 12 hydrogen bonds · protein-protein
- J–K · 1147 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1117 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 1X9F · Hemoglobin Dodecamer from Lumbricus Erythrocruorin · the same entry in another collection · chain L against L, 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 P13579
- Every structure of UniProt P02218
- Every structure of UniProt P11069
- Every structure of UniProt O61233
- Elsewhere: RCSB PDB 1X9F · PDBe 1X9F · UniProt P13579 · UniProt P02218 · UniProt P11069 · UniProt O61233
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