MolNFT v1 · #160687 · protein
Crystal structure of apo PSS1_19B
6PRM · Exo-4S-kappa carrageenan S1 sulfatase: “Crystal structure of apo PSS1_19B”. X-ray diffraction, 1 ligand (CA), 13 pockets (best druggability 0.77). MolNFT v1 #160687 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6PRM
- Type
- protein
- Length
- 1,787 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-4S-kappa carrageenan S1 sulfatase
- Ligands
- CA
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Exo-4S-kappa carrageenan S1 sulfatase | protein | 447 | 33% helix, 17% strand | — |
| D | Exo-4S-kappa carrageenan S1 sulfatase | protein | 446 | 33% helix, 17% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.77 | 0.98 | 29 | empty |
| 2 | 90 | 0.76 | 0.98 | 26 | empty |
| 3 | 799 | 0.69 | 0.76 | 64 | empty |
| 4 | 283 | 0.66 | 0.82 | 43 | empty |
| 5 | 290 | 0.66 | 0.82 | 40 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1527 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1499 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 411 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PRM · Crystal structure of apo PsS1_19B · 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 6PRM · PDBe 6PRM
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