MolNFT v1 · #129181 · protein
Crystal structure of the kappa-carrageenase ZOBELLIA_236 from zobellia galactanivorans
5OCR: “Crystal structure of the kappa-carrageenase ZOBELLIA_236 from zobellia galactanivorans”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.86). MolNFT v1 #129181 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5OCR
- Type
- protein
- Length
- 1,112 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kappa-carrageenase
- EC
- 3.2.1.83
- UniProt
- O84907
- Ligands
- MG
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Kappa-carrageenase (EC 3.2.1.83) | protein | 278 | 9% helix, 47% strand | O84907 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.86 | 0.87 | 100 | GOL |
| 2 | 520 | 0.80 | 0.86 | 53 | GOL |
| 3 | 412 | 0.78 | 0.87 | 43 | GOL |
| 4 | 317 | 0.66 | 0.81 | 34 | empty |
| 5 | 173 | 0.49 | 0.77 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–D · 590 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 540 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 316 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 279 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 159 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5OCR · Crystal structure of the kappa-carrageenase zobellia_236 from Zobellia galactanivorans · 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
- Every structure of UniProt O84907
- Elsewhere: RCSB PDB 5OCR · PDBe 5OCR · UniProt O84907
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