MolNFT v2 · #227671 · protein
Crystal Structure of the Substrate Binding Domain Protein of the ABC Transporter PBP2_YxeM from Vibrio cholerae
9D5W · Amino acid ABC transporter, periplasmic amino acid-binding…: “Crystal Structure of the Substrate Binding Domain Protein of the ABC Transporter PBP2_YxeM from Vibrio…”. X-ray diffraction at 2.3, 3 ligands (K, CL, SO4), 20 pockets…
- PDB
- 9D5W
- Type
- protein
- Length
- 2,043 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Vibrio cholerae O1 biovar El Tor str. N16961
- Molecule
- Amino acid ABC transporter, periplasmic amino acid-binding portion
- UniProt
- Q9KVX8
- Ligands
- K, CL, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.3 · 1 distinct chain · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I | Amino acid ABC transporter, periplasmic amino acid-binding portion | protein | 227 | 39% helix, 28% strand | Q9KVX8 |
Ligands and binding sites
- K · Potassium ion · metal · 6 copies · chains A, B, C, D, E, G
- CL · Chloride ion · ion · 17 copies · chains A, B, C, E, F, H, D, G, I
- SO4 · Sulfate ion · ion · 3 copies · chains D, H, A, G, E
- PGO · S-1,2-propanediol · additive · 9 copies · chains A, D, B, H, G, I
- PGR · R-1,2-propanediol · additive · chains B, C, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.85 | 0.88 | 123 | PGO, SO4, K, CL |
| 2 | 1151 | 0.84 | 0.85 | 125 | PGO, CL, PGR, K |
| 3 | 571 | 0.83 | 0.88 | 93 | PGO, K, CL, SO4 |
| 4 | 567 | 0.73 | 0.81 | 59 | CL |
| 5 | 224 | 0.71 | 0.87 | 38 | PGO, CL, K |
Interfaces
12 interfaces between chains.
- A–E · 951 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 881 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 875 Ų buried · 5 hydrogen bonds · protein-protein
- C–I · 460 Ų buried · 4 hydrogen bonds · protein-protein
- F–H · 453 Ų buried · 3 hydrogen bonds · protein-protein
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 Q9KVX8
- Elsewhere: RCSB PDB 9D5W · PDBe 9D5W · UniProt Q9KVX8
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