Research workbench
Crystal structure of spaa-slh in complex with 4,6-pyr-beta-D-mannacome (P1)
Analyse Crystal structure of spaa-slh in complex with 4,6-pyr-beta-D-mannacome (P1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CWH
- Type
- protein
- Length
- 659 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Surface (S-) layer glycoprotein
- UniProt
- C1JZ07
- Ligands
- 6LA
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Surface (S-) layer glycoprotein | protein | 165 | 42% helix, 5% strand | C1JZ07 |
| C | Surface (S-) layer glycoprotein | protein | 164 | 42% helix, 5% strand | C1JZ07 |
Ligands and binding sites
- 6LA · methyl 2-(acetylamino)-4,6-O-[(1S)-1-carboxyethylidene]-2-deoxy-beta-D-mannopyranoside · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.74 | 0.77 | 101 | empty |
| 2 | 254 | 0.62 | 0.81 | 40 | empty |
| 3 | 309 | 0.62 | 0.79 | 45 | empty |
| 4 | 54 | 0.41 | 0.82 | 14 | 6LA |
| 5 | 71 | 0.32 | 0.75 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–C · 559 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 548 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 418 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 416 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 58 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6CWH · Crystal structure of SpaA-SLH in complex with 4,6-Pyr-beta-D-ManNAcOMe (P1) · 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 C1JZ07
- Elsewhere: RCSB PDB 6CWH · PDBe 6CWH · UniProt C1JZ07
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