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Crystal structure of iota-carrageenase family GH82 from a. fortis in absence of chloride ions
Analyse Crystal structure of iota-carrageenase family GH82 from a. fortis in absence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LMW
- Type
- protein
- Length
- 921 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iota-carrageenase, cgia
- EC
- 3.2.1.157
- UniProt
- Q9F5I8
- Ligands
- CA, NI, NO3
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iota-carrageenase, cgia (EC 3.2.1.157) | protein | 472 | 13% helix, 38% strand | Q9F5I8 |
| B | Iota-carrageenase, cgia (EC 3.2.1.157) | protein | 449 | 13% helix, 39% strand | Q9F5I8 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
- NO3 · Nitrate ion · ion · 4 copies · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.78 | 0.83 | 77 | empty |
| 2 | 428 | 0.68 | 0.80 | 50 | NO3 |
| 3 | 327 | 0.66 | 0.82 | 38 | empty |
| 4 | 298 | 0.52 | 0.74 | 41 | NO3 |
| 5 | 263 | 0.51 | 0.75 | 38 | NO3 |
Interfaces
1 interface between chains.
- A–B · 1009 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3LMW · Crystal structure of iota-carrageenase family GH82 from A. fortis in absence of chloride… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9F5I8 · AlphaFold monomer V2.0 prediction for iota-carrageenase (Q9F5I8) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9F5I8
- Elsewhere: RCSB PDB 3LMW · PDBe 3LMW · UniProt Q9F5I8
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