MolNFT v1 · #124672 · protein
Human histidine triad nucleotide binding protein 1 (hhint) imp complex
5KM0 · Histidine triad nucleotide-binding protein 1: “Human histidine triad nucleotide binding protein 1 (hhint) imp complex”. X-ray diffraction, 1 ligand (IMP), 5 pockets (best druggability 0.59). MolNFT v1 #124672 on GenesisL1: 3D…
- PDB
- 5KM0
- Type
- protein
- Length
- 450 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine triad nucleotide-binding protein 1
- EC
- 3.-.-.-
- UniProt
- P49773
- Ligands
- IMP
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | Histidine triad nucleotide-binding protein 1 (EC 3.-.-.-) | protein | 112 | 29% helix, 25% strand | P49773 |
| A | Histidine triad nucleotide-binding protein 1 (EC 3.-.-.-) | protein | 115 | 29% helix, 24% strand | P49773 |
| D | Histidine triad nucleotide-binding protein 1 (EC 3.-.-.-) | protein | 111 | 30% helix, 25% strand | P49773 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 2 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.59 | 0.88 | 26 | empty |
| 2 | 257 | 0.56 | 0.77 | 49 | empty |
| 3 | 114 | 0.42 | 0.76 | 24 | IMP |
| 4 | 109 | 0.41 | 0.76 | 27 | IMP |
| 5 | 79 | 0.37 | 0.76 | 22 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2004 Ų buried · 44 hydrogen bonds · protein-protein
- B–A · 1999 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 390 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 159 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KM0 · Human Histidine Triad Nucleotide Binding Protein 1 (hHint) IMP complex · the same entry in another collection · chain B against B, 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 P49773
- Elsewhere: RCSB PDB 5KM0 · PDBe 5KM0 · UniProt P49773
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