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Crystal structure of METAP2 modified hemoglobin S
Analyse Crystal structure of METAP2 modified hemoglobin S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K4M
- Type
- protein
- Length
- 1,428 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, A0A481SHK9
- Ligands
- HEM, ACE, CMO
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 8 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin subunit alpha | protein | 141 | 74% helix, 0% strand | P69905 |
| B | Hemoglobin subunit beta | protein | 146 | 76% helix, 0% strand | A0A481SHK9 |
| C, G | Hemoglobin subunit alpha | protein | 140 | 75% helix, 0% strand | P69905 |
| D | Hemoglobin subunit beta | protein | 147 | 77% helix, 0% strand | A0A481SHK9 |
| E | Hemoglobin subunit alpha | protein | 142 | 65% helix, 0% strand | P69905 |
| F | Hemoglobin subunit beta | protein | 146 | 66% helix, 0% strand | A0A481SHK9 |
| H, J | Hemoglobin subunit beta | protein | 143 | 77% helix, 0% strand | A0A481SHK9 |
| I | Hemoglobin subunit alpha | protein | 140 | 67% helix, 0% strand | P69905 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- ACE · Acetyl group · ligand · chains D
- CMO · Carbon monoxide · ion · 9 copies · chains A, B, C, D, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.88 | 0.90 | 100 | empty |
| 2 | 928 | 0.83 | 0.85 | 80 | empty |
| 3 | 1085 | 0.74 | 0.77 | 86 | empty |
| 4 | 218 | 0.73 | 0.88 | 26 | CMO, HEM |
| 5 | 191 | 0.73 | 0.89 | 25 | HEM |
Interfaces
19 interfaces between chains.
- I–J · 994 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 961 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 940 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 932 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 914 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 A0A481SHK9
- Elsewhere: RCSB PDB 7K4M · PDBe 7K4M · UniProt P69905 · UniProt A0A481SHK9
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