MolNFT v1 · #163807 · protein
Xyloglucanase domain of nopaa, a type three effector from sinorhizobium fredii in complex with cellobiose
6SDU · Type III effector nopaa: “Xyloglucanase domain of nopaa, a type three effector from sinorhizobium fredii in complex with cellobiose”. X-ray diffraction, 1 ligand (BGC), 6 pockets (best druggability 0.77). MolNFT v1 #163807 on…
- PDB
- 6SDU
- Type
- protein
- Length
- 877 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type III effector nopaa
- UniProt
- M4PUR5
- Ligands
- BGC
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type III effector nopaa | protein | 222 | 6% helix, 54% strand | M4PUR5 |
| B | Type III effector nopaa | protein | 213 | 6% helix, 51% strand | M4PUR5 |
| C, D | Type III effector nopaa | protein | 221 | 6% helix, 52% strand | M4PUR5 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.77 | 0.80 | 95 | BGC |
| 2 | 131 | 0.49 | 0.79 | 21 | BGC |
| 3 | 82 | 0.47 | 0.82 | 24 | empty |
| 4 | 147 | 0.42 | 0.75 | 29 | empty |
| 5 | 123 | 0.37 | 0.73 | 25 | BGC |
Interfaces
5 interfaces between chains.
- B–C · 599 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 577 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 560 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 508 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 458 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6SDU · Xyloglucanase domain of NopAA, a type three effector from Sinorhizobium fredii in complex… · 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 M4PUR5
- Elsewhere: RCSB PDB 6SDU · PDBe 6SDU · UniProt M4PUR5
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