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Crystal structure of the suca domain of mycobacterium smegmatis kgd after soaking with succinylphosphonate phosphonoethyl ester (pesp)
Analyse Crystal structure of the suca domain of mycobacterium smegmatis kgd after… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R2C
- Type
- protein
- Length
- 3,254 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multifunctional 2-oxoglutarate metabolism enzyme
- EC
- 2.2.1.5, 4.1.1.71, 1.2.4.2, 2.3.1.61
- UniProt
- A0R2B1
- Ligands
- TPP, JQ5, MG, CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multifunctional 2-oxoglutarate metabolism enzyme (EC 2.2.1.5, 4.1.1.71, 1.2.4.2, 2.3.1.61) | protein | 814 | 45% helix, 15% strand | A0R2B1 |
| B | Multifunctional 2-oxoglutarate metabolism enzyme (EC 2.2.1.5, 4.1.1.71, 1.2.4.2, 2.3.1.61) | protein | 815 | 45% helix, 15% strand | A0R2B1 |
| C | Multifunctional 2-oxoglutarate metabolism enzyme (EC 2.2.1.5, 4.1.1.71, 1.2.4.2, 2.3.1.61) | protein | 813 | 45% helix, 15% strand | A0R2B1 |
| D | Multifunctional 2-oxoglutarate metabolism enzyme (EC 2.2.1.5, 4.1.1.71, 1.2.4.2, 2.3.1.61) | protein | 812 | 45% helix, 15% strand | A0R2B1 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, B, C, D
- JQ5 · 4-[ethoxy(oxidanyl)phosphoryl]-4-oxidanylidene-butanoic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1192 | 0.87 | 0.88 | 167 | TPP, MG, JQ5 |
| 2 | 745 | 0.82 | 0.85 | 110 | TPP, MG, JQ5 |
| 3 | 706 | 0.82 | 0.85 | 107 | TPP, MG, JQ5 |
| 4 | 830 | 0.80 | 0.84 | 90 | empty |
| 5 | 751 | 0.76 | 0.81 | 100 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4573 Ų buried · 81 hydrogen bonds · protein-protein
- C–D · 4520 Ų buried · 84 hydrogen bonds · protein-protein
- A–C · 783 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6R2C · Crystal structure of the SucA domain of Mycobacterium smegmatis KGD after soaking with… · 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 A0R2B1
- Elsewhere: RCSB PDB 6R2C · PDBe 6R2C · UniProt A0R2B1
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