Research workbench
MURT/GATD peptidoglycan amidotransferase complex from streptococcus pneumoniae R6
Analyse MURT/GATD peptidoglycan amidotransferase complex from streptococcus pneumoniae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FQB
- Type
- protein
- Length
- 2,504 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mur ligase family protein; Cobyric acid synthase
- EC
- 6.3.2.-, 6.3.5.10
- UniProt
- A0A0B7LND9, A0A062WUX3
- Ligands
- GLN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mur ligase family protein (EC 6.3.2.-) | protein | 383 | 31% helix, 23% strand | A0A0B7LND9 |
| E, F, G, H | Cobyric acid synthase (EC 6.3.5.10) | protein | 247 | 28% helix, 31% strand | A0A062WUX3 |
| B | Mur ligase family protein (EC 6.3.2.-) | protein | 378 | 32% helix, 24% strand | A0A0B7LND9 |
| C | Mur ligase family protein (EC 6.3.2.-) | protein | 375 | 32% helix, 24% strand | A0A0B7LND9 |
| D | Mur ligase family protein (EC 6.3.2.-) | protein | 380 | 32% helix, 24% strand | A0A0B7LND9 |
Ligands and binding sites
- GLN · Glutamine · ligand · 4 copies · chains 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.84 | 0.85 | 145 | GLN |
| 2 | 1026 | 0.83 | 0.84 | 123 | empty |
| 3 | 1111 | 0.83 | 0.84 | 113 | GLN |
| 4 | 1053 | 0.81 | 0.82 | 92 | GLN |
| 5 | 353 | 0.64 | 0.79 | 37 | empty |
Interfaces
11 interfaces between chains.
- C–G · 1331 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1323 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1314 Ų buried · 18 hydrogen bonds · protein-protein
- D–H · 1203 Ų buried · 15 hydrogen bonds · protein-protein
- E–G · 477 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 6FQB · MurT/GatD peptidoglycan amidotransferase complex from Streptococcus pneumoniae R6 · 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 A0A0B7LND9
- Every structure of UniProt A0A062WUX3
- Elsewhere: RCSB PDB 6FQB · PDBe 6FQB · UniProt A0A0B7LND9 · UniProt A0A062WUX3
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