MolNFT v1 · #69305 · protein
Room temperature time-of-flight neutron diffraction study of deoxy human normal adult hemoglobin
3KMF · Hemoglobin subunit alpha: “Room temperature time-of-flight neutron diffraction study of deoxy human normal adult hemoglobin”. Neutron diffraction, 1 ligand (HEM), 10 pockets (best druggability 0.79). MolNFT v1 #69305 on GenesisL1…
- PDB
- 3KMF
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- neutron diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HEM
- Pockets
- 10 · best druggability 0.79
Structure
neutron diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Hemoglobin subunit alpha | protein | 141 | 73% helix, 0% strand | P69905 |
| C, G | Hemoglobin subunit beta | protein | 146 | 77% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.79 | 0.81 | 76 | empty |
| 2 | 257 | 0.75 | 0.88 | 29 | HEM |
| 3 | 279 | 0.74 | 0.87 | 29 | HEM |
| 4 | 287 | 0.74 | 0.86 | 30 | HEM |
| 5 | 285 | 0.72 | 0.85 | 30 | HEM |
Interfaces
5 interfaces between chains.
- A–C · 848 Ų buried · 10 hydrogen bonds · protein-protein
- E–G · 832 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 707 Ų buried · 8 hydrogen bonds · protein-protein
- A–G · 693 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 310 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3KMF · Room Temperature Time-of-Flight Neutron Diffraction Study of Deoxy Human Normal Adult… · 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 3KMF · PDBe 3KMF · UniProt P69905 · UniProt P68871
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