MolNFT v1 · #127022 · protein
Crystal structure of the rrga JO.IN complex
5MKC · Cell wall surface anchor family protein (JO),CELL wall…: “Crystal structure of the rrga JO.IN complex”. X-ray diffraction, 3 ligands (NI, CA, SO4), 9 pockets (best druggability 0.88). MolNFT v1 #127022 on GenesisL1: 3D structure…
- PDB
- 5MKC
- Type
- protein
- Length
- 1,240 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell wall surface anchor family protein (JO),CELL wall surface anchor family protein (in)
- UniProt
- A0A0Y1GQ57, A0A0U0F558
- Ligands
- NI, CA, SO4
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell wall surface anchor family protein (JO),CELL wall surface anchor family protein (in) | protein | 207 | 3% helix, 54% strand | A0A0Y1GQ57, A0A0U0F558 |
| B, C | Cell wall surface anchor family protein (JO),CELL wall surface anchor family protein (in) | protein | 206 | 3% helix, 53% strand | A0A0Y1GQ57, A0A0U0F558 |
| D, E, F | Cell wall surface anchor family protein (JO),CELL wall surface anchor family protein (in) | protein | 207 | 3% helix, 54% strand | A0A0Y1GQ57, A0A0U0F558 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains A, D, F
- CA · Calcium ion · metal · 3 copies · chains C, E, F
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.88 | 0.89 | 110 | empty |
| 2 | 682 | 0.86 | 0.90 | 73 | empty |
| 3 | 458 | 0.82 | 0.90 | 50 | empty |
| 4 | 526 | 0.80 | 0.86 | 58 | empty |
| 5 | 209 | 0.76 | 0.91 | 28 | empty |
Interfaces
8 interfaces between chains.
- D–F · 661 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 634 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 624 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 624 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 616 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 isopeptide (isopeptide).
Compared structures
- 5MKC · Crystal structure of the RrgA Jo.In complex · 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 A0A0Y1GQ57
- Every structure of UniProt A0A0U0F558
- Elsewhere: RCSB PDB 5MKC · PDBe 5MKC · UniProt A0A0Y1GQ57 · UniProt A0A0U0F558
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