Research workbench
Surface-layer (S-layer) rsaa protein from caulobacter crescentus bound to strontium and iodide
Analyse Surface-layer (S-layer) rsaa protein from caulobacter crescentus bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P5T
- Type
- protein
- Length
- 4,682 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-layer protein
- UniProt
- P35828
- Ligands
- SR, IOD
- Pockets
- 10 · best druggability 0.44
Structure
x-ray diffraction · 4 distinct chains · 1% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | S-layer protein | protein | 782 | 2% helix, 46% strand | P35828 |
| B | S-layer protein | protein | 776 | 2% helix, 45% strand | P35828 |
| C, E | S-layer protein | protein | 781 | 1% helix, 46% strand | P35828 |
| D | S-layer protein | protein | 780 | 1% helix, 46% strand | P35828 |
Ligands and binding sites
- SR · Strontium ion · metal · 124 copies · chains A, B, C, D, E, F
- IOD · Iodide ion · ion · 150 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.44 | 0.74 | 32 | IOD |
| 2 | 142 | 0.40 | 0.74 | 28 | SR |
| 3 | 123 | 0.38 | 0.74 | 23 | empty |
| 4 | 58 | 0.37 | 0.80 | 16 | empty |
| 5 | 54 | 0.35 | 0.79 | 15 | empty |
Interfaces
7 interfaces between chains.
- B–D · 362 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 358 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 354 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 342 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 171 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6P5T · Surface-layer (S-layer) RsaA protein from Caulobacter crescentus bound to strontium and… · the same entry in another collection · chain F against F, TM-score 1.00
- P35828 · AlphaFold monomer V2.0 prediction for S-layer protein (P35828) · a predicted model of the same protein · chain B 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 P35828
- Elsewhere: RCSB PDB 6P5T · PDBe 6P5T · UniProt P35828
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