Research workbench
Crystal Structure of the GatD/MurT Enzyme Complex from Staphylococcus aureus
Analyse Crystal Structure of the GatD/MurT Enzyme Complex from Staphylococcus aureus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GS2
- Type
- protein
- Length
- 1,262 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.04
- Source
- Staphylococcus aureus; Staphylococcus aureus (strain N315)
- Molecule
- SA1707 protein; SA1708 protein
- UniProt
- A0A0H3JN63, A0A0H3JUU7
- Ligands
- ZN, MG
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.04 · 4 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SA1707 protein | protein | 246 | 34% helix, 29% strand | A0A0H3JN63 |
| B | SA1708 protein | protein | 389 | 36% helix, 24% strand | A0A0H3JUU7 |
| C | SA1707 protein | protein | 243 | 31% helix, 31% strand | A0A0H3JN63 |
| D | SA1708 protein | protein | 384 | 37% helix, 24% strand | A0A0H3JUU7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, D
- MG · Magnesium ion · metal · chains B
- 144 · Tris-hydroxymethyl-methyl-ammonium · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.76 | 0.86 | 47 | empty |
| 2 | 1180 | 0.74 | 0.77 | 103 | empty |
| 3 | 369 | 0.70 | 0.82 | 57 | empty |
| 4 | 93 | 0.38 | 0.76 | 18 | empty |
| 5 | 75 | 0.37 | 0.77 | 25 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1328 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 995 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 993 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 467 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 372 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6GS2 · Crystal structure of the GATD/MURT enzyme complex from staphylococcus aureus · 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 A0A0H3JN63
- Every structure of UniProt A0A0H3JUU7
- Elsewhere: RCSB PDB 6GS2 · PDBe 6GS2 · UniProt A0A0H3JN63 · UniProt A0A0H3JUU7
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