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New crystal form structure of human NCS1
Analyse New crystal form structure of human NCS1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GUK
- Type
- protein
- Length
- 724 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuronal calcium sensor 1
- UniProt
- P62166
- Ligands
- P2G, P3G, ALA, CA, NA
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuronal calcium sensor 1 | protein | 183 | 62% helix, 5% strand | P62166 |
| C | Neuronal calcium sensor 1 | protein | 182 | 63% helix, 4% strand | P62166 |
| B | Neuronal calcium sensor 1 | protein | 179 | 63% helix, 4% strand | P62166 |
| D | Neuronal calcium sensor 1 | protein | 180 | 63% helix, 6% strand | P62166 |
Ligands and binding sites
- P2G · (2s,4r,6r,6as)-4-(2-amino-6-oxo-1,6-dihydropurin-9-yl)-6-(hydroxymethyl)-tetrahydrofuro[3,4-d][1,3]dioxol-2-ylphosphoni C acid · ligand · 4 copies · chains C, B, D
- P3G · 3,6,9,12,15-pentaoxaheptadecane · ligand · chains C
- ALA · Alanine · ligand · chains B
- CA · Calcium ion · metal · 12 copies · chains A, C, B, D
- NA · Sodium ion · metal · 4 copies · chains A, C, B, D
- PG4 · Tetraethylene glycol · additive · 7 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.71 | 0.76 | 50 | PG4, EDO |
| 2 | 531 | 0.69 | 0.78 | 51 | PG4, EDO, P2G |
| 3 | 507 | 0.69 | 0.78 | 48 | PG4, P2G |
| 4 | 600 | 0.67 | 0.76 | 47 | EDO, P2G, PG4 |
| 5 | 142 | 0.43 | 0.76 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–D · 262 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 257 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 100 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 70 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 69 Ų buried · 0 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 P62166
- Elsewhere: RCSB PDB 4GUK · PDBe 4GUK · UniProt P62166
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