Research workbench
Crystal structure of metal-citrate-binding protein (mcta) of ABC transporter endogenously bound to MG2+-citrate complex (form I)
Analyse Crystal structure of metal-citrate-binding protein (mcta) of ABC transporter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F6E
- Type
- protein
- Length
- 1,017 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron ABC transporter, periplasmic iron-binding protein
- UniProt
- Q53VZ2
- Ligands
- 2OP, MG, CL, CO2
- Pockets
- 12 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron ABC transporter, periplasmic iron-binding protein | protein | 340 | 46% helix, 17% strand | Q53VZ2 |
| B | Iron ABC transporter, periplasmic iron-binding protein | protein | 341 | 47% helix, 17% strand | Q53VZ2 |
| C | Iron ABC transporter, periplasmic iron-binding protein | protein | 336 | 47% helix, 18% strand | Q53VZ2 |
Ligands and binding sites
- 2OP · (2S)-2-hydroxypropanoic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 8 copies · chains A, B
- CO2 · Carbon dioxide · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, C, B
- GOL · Glycerol · additive · 7 copies · chains A, B, C
- CIT · Citric acid · additive · 3 copies · chains A, B, C
- PGO · S-1,2-propanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.53 | 0.77 | 26 | PGO |
| 2 | 178 | 0.47 | 0.76 | 26 | empty |
| 3 | 100 | 0.43 | 0.78 | 17 | empty |
| 4 | 122 | 0.43 | 0.77 | 17 | CL |
| 5 | 70 | 0.42 | 0.81 | 20 | MG, CIT |
Interfaces
3 interfaces between chains.
- A–B · 694 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 201 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 15 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7F6E · Crystal structure of metal-citrate-binding protein (MctA) of ABC transporter endogenously… · 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 Q53VZ2
- Elsewhere: RCSB PDB 7F6E · PDBe 7F6E · UniProt Q53VZ2
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