Research workbench
Structure in P3212 form of the PBP/SBP moaa in complex with mannopinic acid from A.TUMEFACIEN R10
Analyse Structure in P3212 form of the PBP/SBP moaa in complex with mannopinic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TFQ
- Type
- protein
- Length
- 986 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter substrate-binding protein
- UniProt
- O50271
- Ligands
- N72, GLC, SO4, CL
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ABC transporter substrate-binding protein | protein | 493 | 31% helix, 26% strand | O50271 |
Ligands and binding sites
- N72 · (2~{R})-2-[[(3~{R},4~{R},5~{S})-3,4,5,6-tetrakis(oxidanyl)-2-oxidanylidene-hexyl]amino]pentanedioic acid · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 26 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
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 | 169 | 0.80 | 0.96 | 47 | N72, CL |
| 2 | 164 | 0.79 | 0.95 | 40 | N72 |
| 3 | 1016 | 0.77 | 0.79 | 113 | CL |
| 4 | 1086 | 0.76 | 0.79 | 107 | empty |
| 5 | 55 | 0.44 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 806 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 6TFQ · Structure in P3212 form of the PBP/SBP MoaA in complex with mannopinic acid from… · 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 O50271
- Elsewhere: RCSB PDB 6TFQ · PDBe 6TFQ · UniProt O50271
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