Research workbench
X-ray structure of a new fully ligated carbomonoxy form of trematomus newnesi hemoglobin (HB1TNCO).
Analyse X-ray structure of a new fully ligated carbomonoxy form of trematomus newnesi… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LFG
- Type
- protein
- Length
- 572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha-1; Hemoglobin subunit beta-1/2
- UniProt
- P45718, P45720
- Ligands
- HEM, ACE, CMO
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha-1 | protein | 142 | 77% helix, 0% strand | P45718 |
| B | Hemoglobin subunit beta-1/2 | protein | 146 | 76% helix, 0% strand | P45720 |
| D | Hemoglobin subunit beta-1/2 | protein | 142 | 76% helix, 0% strand | P45720 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- ACE · Acetyl group · 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
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 | 308 | 0.73 | 0.85 | 39 | CMO, HEM |
| 2 | 261 | 0.73 | 0.86 | 27 | CMO, HEM |
| 3 | 233 | 0.72 | 0.87 | 28 | HEM, CMO |
| 4 | 215 | 0.71 | 0.87 | 29 | CMO, HEM |
| 5 | 207 | 0.51 | 0.76 | 30 | empty |
Interfaces
3 interfaces between chains.
- C–D · 846 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 842 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 296 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5LFG · X-ray structure of a new fully ligated carbomonoxy form of Trematomus newnesi hemoglobin… · the same entry in another collection · chain A against A, TM-score 1.00
- P45718 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha-1 (P45718) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P45720 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta-1/2 (P45720) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P45718
- Every structure of UniProt P45720
- Elsewhere: RCSB PDB 5LFG · PDBe 5LFG · UniProt P45718 · UniProt P45720
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