MolNFT v1 · #126277 · protein
Crystal structure of ruminococcus flavefaciens scaffoldin C cohesin in complex with a dockerin from an uncharacterized cbm-containing protein
5LXV: “Crystal structure of ruminococcus flavefaciens scaffoldin C cohesin in complex with a dockerin from an…”. X-ray diffraction, 1 ligand (CA), 1 pocket (best druggability 0.60). MolNFT v1 #126277 on GenesisL1: 3D structure, binding…
- PDB
- 5LXV
- Type
- protein
- Length
- 475 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scaffoldin C; Carbohydrate-binding protein WP_009985128
- UniProt
- G9FCX2
- Ligands
- CA
- Pockets
- 1 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Scaffoldin C | protein | 172 | 10% helix, 49% strand | G9FCX2 |
| B, D | Carbohydrate-binding protein WP_009985128 | protein | 65 | 45% helix, 0% strand | — |
| C | Scaffoldin C | protein | 173 | 10% helix, 49% strand | G9FCX2 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.60 | 0.74 | 66 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1429 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1402 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 215 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5LXV · Crystal structure of Ruminococcus flavefaciens scaffoldin C cohesin in complex with a… · 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 G9FCX2
- Elsewhere: RCSB PDB 5LXV · PDBe 5LXV · UniProt G9FCX2
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