Research workbench
Crystal structure of the H101A mutant echint gmp complex
Analyse Crystal structure of the H101A mutant echint gmp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N1T
- Type
- protein
- Length
- 458 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hit-like protein hint
- UniProt
- P0ACE7
- Ligands
- 5GP
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hit-like protein hint | protein | 114 | 29% helix, 25% strand | P0ACE7 |
| B | Hit-like protein hint | protein | 117 | 28% helix, 22% strand | P0ACE7 |
| E | Hit-like protein hint | protein | 112 | 29% helix, 25% strand | P0ACE7 |
| F | Hit-like protein hint | protein | 115 | 29% helix, 24% strand | P0ACE7 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 4 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.73 | 0.84 | 48 | empty |
| 2 | 140 | 0.53 | 0.80 | 25 | 5GP |
| 3 | 163 | 0.52 | 0.79 | 29 | 5GP |
| 4 | 147 | 0.50 | 0.79 | 29 | 5GP |
| 5 | 127 | 0.49 | 0.79 | 28 | 5GP |
Interfaces
5 interfaces between chains.
- A–B · 2097 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 2055 Ų buried · 39 hydrogen bonds · protein-protein
- B–E · 490 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 36 Ų buried · 0 hydrogen bonds · protein-protein
- B–F · 25 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3N1T · Crystal structure of the H101A mutant ecHint GMP complex · the same entry in another collection · chain F against F, TM-score 1.00
- P0ACE7 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphoramidase (P0ACE7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0ACE7
- Elsewhere: RCSB PDB 3N1T · PDBe 3N1T · UniProt P0ACE7
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