MolNFT v1 · #177105 · protein
Crystal structure analysis of the streptococcus agalactiae ribose binding protein rbsb
7E7M · D-ribose ABC transporter substrate-binding protein: “Crystal structure analysis of the streptococcus agalactiae ribose binding protein rbsb”. X-ray diffraction, 1 ligand (RIP), 9 pockets (best druggability 0.78). MolNFT v1 #177105…
- PDB
- 7E7M
- Type
- protein
- Length
- 1,120 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-ribose ABC transporter substrate-binding protein
- UniProt
- A0A6H3FYP2
- Ligands
- RIP
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-ribose ABC transporter substrate-binding protein | protein | 283 | 42% helix, 22% strand | A0A6H3FYP2 |
| B | D-ribose ABC transporter substrate-binding protein | protein | 280 | 44% helix, 21% strand | A0A6H3FYP2 |
| C | D-ribose ABC transporter substrate-binding protein | protein | 284 | 46% helix, 20% strand | A0A6H3FYP2 |
| D | D-ribose ABC transporter substrate-binding protein | protein | 273 | 45% helix, 19% strand | A0A6H3FYP2 |
Ligands and binding sites
- RIP · beta-D-ribopyranose · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 760 | 0.78 | 0.82 | 81 | empty |
| 2 | 265 | 0.70 | 0.85 | 37 | empty |
| 3 | 479 | 0.69 | 0.80 | 48 | empty |
| 4 | 354 | 0.58 | 0.76 | 44 | empty |
| 5 | 84 | 0.50 | 0.83 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 645 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 598 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 453 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 451 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 72 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7E7M · Crystal Structure Analysis of the Streptococcus agalactiae Ribose Binding Protein RbsB · the same entry in another collection · chain D against D, 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 A0A6H3FYP2
- Elsewhere: RCSB PDB 7E7M · PDBe 7E7M · UniProt A0A6H3FYP2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.