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The crystal structure of the poly-alpha-L-glutamate peptides synthetase rimk at 2.05 ångström resolution.
Analyse The crystal structure of the poly-alpha-L-glutamate peptides synthetase rimk at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZCT
- Type
- protein
- Length
- 2,334 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein S6--L-glutamate ligase
- EC
- 6.3.2.-
- UniProt
- P0C0U4
- Ligands
- ANP, MG, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G, H | Ribosomal protein S6--L-glutamate ligase (EC 6.3.2.-) | protein | 292 | 37% helix, 29% strand | P0C0U4 |
| C | Ribosomal protein S6--L-glutamate ligase (EC 6.3.2.-) | protein | 290 | 37% helix, 29% strand | P0C0U4 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.79 | 0.83 | 76 | SO4, ANP, MG |
| 2 | 802 | 0.79 | 0.82 | 77 | ANP, MG, SO4 |
| 3 | 800 | 0.79 | 0.82 | 75 | ANP, MG, SO4 |
| 4 | 791 | 0.78 | 0.82 | 77 | ANP, MG, SO4 |
| 5 | 726 | 0.78 | 0.82 | 73 | ANP, MG |
Interfaces
11 interfaces between chains.
- A–B · 2339 Ų buried · 33 hydrogen bonds · protein-protein
- G–H · 2321 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2303 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2179 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 676 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5ZCT · The crystal structure of the poly-alpha-L-glutamate peptides synthetase RimK at 2.05… · the same entry in another collection · chain D against D, TM-score 1.00
- P0C0U4 · AlphaFold monomer V2.0 prediction for ribosomal protein S6-- L-glutamate ligase (P0C0U4) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P0C0U4
- Elsewhere: RCSB PDB 5ZCT · PDBe 5ZCT · UniProt P0C0U4
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