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Crystal structure of metal-citrate-binding protein (mcta) of ABC transporter endogenously bound to citrate
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
- 7F6K
- Type
- protein
- Length
- 1,003 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
- CL, CO2, SO4
- Pockets
- 9 · best druggability 0.51
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 | 336 | 47% helix, 18% strand | Q53VZ2 |
| B | Iron ABC transporter, periplasmic iron-binding protein | protein | 337 | 47% helix, 18% strand | Q53VZ2 |
| C | Iron ABC transporter, periplasmic iron-binding protein | protein | 330 | 48% helix, 18% strand | Q53VZ2 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B, C
- CO2 · Carbon dioxide · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains B
- CIT · Citric acid · additive · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.51 | 0.76 | 33 | empty |
| 2 | 206 | 0.51 | 0.76 | 27 | empty |
| 3 | 201 | 0.47 | 0.75 | 26 | empty |
| 4 | 134 | 0.44 | 0.77 | 17 | empty |
| 5 | 69 | 0.43 | 0.81 | 21 | CIT |
Interfaces
2 interfaces between chains.
- A–B · 718 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 199 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7F6K · Crystal structure of metal-citrate-binding protein (MctA) of ABC transporter endogenously… · the same entry in another collection · chain B against B, 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 7F6K · PDBe 7F6K · UniProt Q53VZ2
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