Research workbench
Crystal structure of mn-dependent gme hnh nicking endonuclease from geobacter metallireducens gs-15, northeast structural genomics consortium (nesg) target GMR87
Analyse Crystal structure of mn-dependent gme hnh nicking endonuclease from geobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H9D
- Type
- protein
- Length
- 268 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hnh endonuclease
- UniProt
- Q39X46
- Ligands
- ZN, MG
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hnh endonuclease | protein | 97 | 47% helix, 12% strand | Q39X46 |
| B | Hnh endonuclease | protein | 90 | 50% helix, 13% strand | Q39X46 |
| C | Hnh endonuclease | protein | 81 | 43% helix, 15% strand | Q39X46 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.56 | 0.75 | 31 | MG |
| 2 | 184 | 0.45 | 0.74 | 25 | empty |
| 3 | 154 | 0.44 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 836 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 346 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 166 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 4H9D · Crystal Structure of Mn-dependent Gme HNH nicking endonuclease from Geobacter… · 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 Q39X46
- Elsewhere: RCSB PDB 4H9D · PDBe 4H9D · UniProt Q39X46
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