Research workbench
Crystal structure of riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.
Analyse Crystal structure of riftia pachyptila C1 hemoglobin reveals novel assembly of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YHU
- Type
- protein
- Length
- 3,516 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin A1 chain; Giant hemoglobins B chain; Hemoglobin B1A chain; Hemoglobin B2 chain
- UniProt
- Q8IFK4, P80592, Q8IFK2, Q8IFJ9
- Ligands
- HEM, ZN, OXY
- 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, M, Q, U | Hemoglobin A1 chain | protein | 145 | 77% helix, 0% strand | Q8IFK4 |
| B, F, J, N, R, V | Giant hemoglobins B chain | protein | 144 | 76% helix, 0% strand | P80592 |
| C, G, K, O, S, W | Hemoglobin B1A chain | protein | 148 | 76% helix, 0% strand | Q8IFK2 |
| D, H, L, P, T, X | Hemoglobin B2 chain | protein | 149 | 74% helix, 0% strand | Q8IFJ9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 24 copies · chains A, C, B, D, E, G, F, H, I, K, J, L, M, O, N, P, Q, S, R, T, U, W, V, X
- ZN · Zinc ion · metal · 12 copies · chains B, J, F, N, V, R
- OXY · Oxygen molecule · ion · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
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 | 965 | 0.85 | 0.86 | 100 | HEM, OXY |
| 2 | 1160 | 0.85 | 0.86 | 122 | HEM, OXY |
| 3 | 1126 | 0.85 | 0.86 | 118 | HEM, OXY |
| 4 | 978 | 0.84 | 0.85 | 70 | HEM, OXY |
| 5 | 948 | 0.84 | 0.85 | 79 | HEM, OXY |
Interfaces
51 interfaces between chains.
- B–D · 1105 Ų buried · 9 hydrogen bonds · protein-protein
- N–P · 1098 Ų buried · 9 hydrogen bonds · protein-protein
- R–T · 1098 Ų buried · 8 hydrogen bonds · protein-protein
- V–X · 1098 Ų buried · 8 hydrogen bonds · protein-protein
- J–L · 1097 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 1YHU · Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24… · the same entry in another collection · chain J against J, 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 Q8IFK4
- Every structure of UniProt P80592
- Every structure of UniProt Q8IFK2
- Every structure of UniProt Q8IFJ9
- Elsewhere: RCSB PDB 1YHU · PDBe 1YHU · UniProt Q8IFK4 · UniProt P80592 · UniProt Q8IFK2 · UniProt Q8IFJ9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.