Research workbench
Oxy-deoxy intermediate of V2 hemoglobin at 69% oxygen saturation
Analyse Oxy-deoxy intermediate of V2 hemoglobin at 69% oxygen saturation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VLD
- Type
- protein
- Length
- 1,174 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular A1 globin; Extracellular A2 globin; Extracellular B2 globin; Extracellular…
- UniProt
- S0BBU7, S0BBR6, S0BCU7, S0BAP9
- Ligands
- HEM, NAG, FUC, CA, OXY
- Pockets
- 17 · 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 | Extracellular A1 globin | protein | 146 | 82% helix, 0% strand | S0BBU7 |
| B, F | Extracellular A2 globin | protein | 144 | 77% helix, 0% strand | S0BBR6 |
| C, G | Extracellular B2 globin | protein | 149 | 70% helix, 0% strand | S0BCU7 |
| D, H | Extracellular B1 globin | protein | 148 | 74% helix, 0% strand | S0BAP9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, D, B, C, E, H, F, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains D, H
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, D, E, H
- CA · Calcium ion · metal · 2 copies · chains B, F
- OXY · Oxygen molecule · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.85 | 0.86 | 91 | HEM, OXY |
| 2 | 845 | 0.84 | 0.86 | 74 | HEM, OXY |
| 3 | 813 | 0.84 | 0.86 | 75 | HEM, OXY |
| 4 | 839 | 0.83 | 0.85 | 71 | HEM, OXY |
| 5 | 591 | 0.71 | 0.79 | 69 | empty |
Interfaces
13 interfaces between chains.
- F–G · 1167 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1159 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1113 Ų buried · 6 hydrogen bonds · protein-protein
- E–H · 1081 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 689 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7VLD · Oxy-deoxy intermediate of V2 hemoglobin at 69% oxygen saturation · the same entry in another collection · chain D against D, 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 S0BBU7
- Every structure of UniProt S0BBR6
- Every structure of UniProt S0BCU7
- Every structure of UniProt S0BAP9
- Elsewhere: RCSB PDB 7VLD · PDBe 7VLD · UniProt S0BBU7 · UniProt S0BBR6 · UniProt S0BCU7 · UniProt S0BAP9
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