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Crystal structure of wild type echint gmp complex
Analyse Crystal structure of wild type 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
- 3N1S
- Type
- protein
- Length
- 931 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hit-like protein hint
- UniProt
- P0ACE7
- Ligands
- 5GP
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hit-like protein hint | protein | 117 | 28% helix, 24% strand | P0ACE7 |
| B, F | Hit-like protein hint | protein | 118 | 29% helix, 22% strand | P0ACE7 |
| E | Hit-like protein hint | protein | 115 | 29% helix, 24% strand | P0ACE7 |
| I | Hit-like protein hint | protein | 114 | 27% helix, 23% strand | P0ACE7 |
| J | Hit-like protein hint | protein | 119 | 29% helix, 24% strand | P0ACE7 |
| M, N | Hit-like protein hint | protein | 115 | 30% helix, 24% strand | P0ACE7 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 8 copies · chains A, J, B, E, F, I, M, N
- EDO · 1,2-ethanediol · additive · 25 copies · chains A, B, I, J, E, F, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.79 | 0.81 | 84 | 5GP, EDO |
| 2 | 705 | 0.74 | 0.80 | 79 | 5GP, EDO |
| 3 | 385 | 0.63 | 0.78 | 42 | empty |
| 4 | 118 | 0.42 | 0.76 | 27 | EDO, 5GP |
| 5 | 102 | 0.38 | 0.75 | 23 | 5GP, EDO |
Interfaces
13 interfaces between chains.
- A–B · 2146 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 2113 Ų buried · 44 hydrogen bonds · protein-protein
- I–J · 2084 Ų buried · 40 hydrogen bonds · protein-protein
- M–N · 2078 Ų buried · 41 hydrogen bonds · protein-protein
- A–J · 274 Ų buried · 1 hydrogen bond · 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 P0ACE7
- Elsewhere: RCSB PDB 3N1S · PDBe 3N1S · UniProt P0ACE7
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