Research workbench
Structure in P21 form of the PBP/SBP moaa in complex with mannopinic acid from A.TUMEFACIEN R10
Analyse Structure in P21 form of the PBP/SBP moaa in complex with mannopinic acid from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TFX
- Type
- protein
- Length
- 987 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, MG
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter substrate-binding protein | protein | 493 | 32% helix, 26% strand | O50271 |
| B | ABC transporter substrate-binding protein | protein | 494 | 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
- MG · Magnesium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.82 | 0.83 | 130 | EDO |
| 2 | 177 | 0.81 | 0.97 | 42 | N72 |
| 3 | 180 | 0.81 | 0.96 | 49 | N72 |
| 4 | 605 | 0.67 | 0.77 | 72 | EDO |
| 5 | 61 | 0.44 | 0.82 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 957 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6TFX · Structure in P21 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 6TFX · PDBe 6TFX · UniProt O50271
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