Research workbench
Crystal structure of human NM23-H1
Analyse Crystal structure of human NM23-H1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L7U
- Type
- protein
- Length
- 458 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase a
- EC
- 2.7.4.6
- UniProt
- P15531
- Ligands
- PO4
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nucleoside diphosphate kinase a (EC 2.7.4.6) | protein | 152 | 48% helix, 16% strand | P15531 |
| B | Nucleoside diphosphate kinase a (EC 2.7.4.6) | protein | 154 | 51% helix, 16% strand | P15531 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.66 | 0.82 | 33 | empty |
| 2 | 180 | 0.46 | 0.75 | 27 | empty |
| 3 | 185 | 0.45 | 0.75 | 29 | empty |
| 4 | 91 | 0.45 | 0.80 | 27 | empty |
| 5 | 161 | 0.44 | 0.75 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 835 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 820 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 811 Ų buried · 7 hydrogen bonds · protein-protein
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 P15531
- Elsewhere: RCSB PDB 3L7U · PDBe 3L7U · UniProt P15531
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