Research workbench
Carbonmonoxy hemoglobin in complex with the antisickling agent methyl 2-((2-formyl-3-HYDROXYPHENOXY)METHYL)NICOTINATE
Analyse Carbonmonoxy hemoglobin in complex with the antisickling agent methyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XE7
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HEM, V2D, CMO
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 74% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 146 | 75% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- V2D · methyl 2-[(3-hydroxy-2-methylphenoxy)methyl]pyridine-3-carboxylate · ligand · 2 copies · chains A, C
- CMO · Carbon monoxide · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.82 | 0.90 | 64 | empty |
| 2 | 234 | 0.74 | 0.88 | 28 | CMO, HEM |
| 3 | 218 | 0.73 | 0.88 | 29 | CMO, HEM |
| 4 | 185 | 0.69 | 0.87 | 24 | CMO, HEM |
| 5 | 178 | 0.69 | 0.88 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 926 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 918 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 465 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 425 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 396 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6XE7 · Carbonmonoxy hemoglobin in complex with the antisickling agent methyl… · the same entry in another collection · chain D against D, TM-score 1.00
- P68871 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P68871) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P69905 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P69905) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 6XE7 · PDBe 6XE7 · UniProt P69905 · UniProt P68871
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