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Crystal structure of an amino acid ABC transporter substrate-binding protein from streptococcus pneumoniae canada MDR_19A bound to L- arginine, form 1
Analyse Crystal structure of an amino acid ABC transporter substrate-binding protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H5F
- Type
- protein
- Length
- 959 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amino acid ABC superfamily ATP binding cassette transporter, binding protein
- UniProt
- D6ZRZ2
- Ligands
- ARG, SO4, CL
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Amino acid ABC superfamily ATP binding cassette transporter, binding protein | protein | 240 | 40% helix, 23% strand | D6ZRZ2 |
| D | Amino acid ABC superfamily ATP binding cassette transporter, binding protein | protein | 239 | 38% helix, 25% strand | D6ZRZ2 |
Ligands and binding sites
- ARG · Arginine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, C, B
- CL · Chloride ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 19 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 7 copies · chains B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, C, B, D
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.69 | 0.76 | 69 | empty |
| 2 | 329 | 0.59 | 0.77 | 38 | EDO, GOL |
| 3 | 457 | 0.57 | 0.73 | 51 | PEG |
| 4 | 314 | 0.56 | 0.76 | 45 | GOL |
| 5 | 77 | 0.38 | 0.77 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–C · 812 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 734 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 609 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 340 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 266 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4H5F · Crystal structure of an amino acid ABC transporter substrate-binding protein 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 D6ZRZ2
- Elsewhere: RCSB PDB 4H5F · PDBe 4H5F · UniProt D6ZRZ2
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