Research workbench
NCTC10712
Analyse NCTC10712 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EFF
- Type
- protein
- Length
- 819 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NCTC10712 siglec
- Ligands
- CA
- Pockets
- 9 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NCTC10712 siglec | protein | 203 | 11% helix, 35% strand | — |
| B | NCTC10712 siglec | protein | 206 | 12% helix, 34% strand | — |
| C | NCTC10712 siglec | protein | 205 | 12% helix, 34% strand | — |
| D | NCTC10712 siglec | protein | 205 | 12% helix, 35% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 18 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains B
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 | 266 | 0.56 | 0.77 | 27 | empty |
| 2 | 221 | 0.46 | 0.74 | 30 | GOL |
| 3 | 204 | 0.46 | 0.74 | 22 | GOL |
| 4 | 178 | 0.44 | 0.74 | 28 | empty |
| 5 | 88 | 0.36 | 0.76 | 15 | GOL |
Interfaces
4 interfaces between chains.
- A–B · 501 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 499 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 447 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 184 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6EFF · NCTC10712 · 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
- Elsewhere: RCSB PDB 6EFF · PDBe 6EFF
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