MolNFT v1 · #1649 · protein
Human deoxyhaemoglobin-2,3-diphosphoglycerate complex
1B86 · Protein (hemoglobin: “Human deoxyhaemoglobin-2,3-diphosphoglycerate complex”. X-ray diffraction, 3 ligands (HEM, DG2, OXY), 8 pockets (best druggability 0.79). MolNFT v1 #1649 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1B86
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (hemoglobin
- UniProt
- P69905, P68871
- Ligands
- HEM, DG2, OXY
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein (hemoglobin | protein | 141 | 77% helix, 0% strand | P69905 |
| B, D | Protein (hemoglobin | protein | 146 | 76% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- DG2 · (2R)-2,3-diphosphoglyceric acid · ligand · chains B, D
- OXY · Oxygen molecule · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.79 | 0.81 | 84 | empty |
| 2 | 258 | 0.74 | 0.87 | 29 | HEM, OXY |
| 3 | 247 | 0.73 | 0.86 | 30 | HEM, OXY |
| 4 | 215 | 0.72 | 0.87 | 28 | HEM |
| 5 | 217 | 0.72 | 0.87 | 27 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 874 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 865 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 709 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 696 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 288 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1B86 · Human deoxyhaemoglobin-2,3-diphosphoglycerate complex · 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 P69905
- Every structure of UniProt P68871
- Elsewhere: RCSB PDB 1B86 · PDBe 1B86 · UniProt P69905 · UniProt P68871
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