MolNFT v1 · #162216 · protein
Crystal structure of the suca domain of mycobacterium smegmatis kgd after soaking with succinylphosphonate phosphonoethyl ester, followed by temperature increase
6R2D · Multifunctional 2-oxoglutarate metabolism enzyme: “Crystal structure of the suca domain of mycobacterium smegmatis kgd after soaking with succinylphosphonate…”. X-ray diffraction, 3 ligands (ZP1, MG, CA), 20 pockets (best…
- PDB
- 6R2D
- Type
- protein
- Length
- 3,245 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
- ZP1, 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 | 812 | 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 | 808 | 44% 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 | 811 | 45% helix, 15% strand | A0R2B1 |
Ligands and binding sites
- ZP1 · (4~{S})-4-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy) phosphoryl]oxyethyl]-2~{H}-1,3-thiazol-2-yl]-4-[ethoxy(oxidanyl)phosphoryl]-4-oxidanyl-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 | 1057 | 0.87 | 0.89 | 155 | ZP1, MG |
| 2 | 1154 | 0.87 | 0.89 | 159 | ZP1, MG |
| 3 | 1053 | 0.80 | 0.81 | 100 | empty |
| 4 | 800 | 0.74 | 0.79 | 99 | empty |
| 5 | 587 | 0.72 | 0.79 | 56 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4529 Ų buried · 83 hydrogen bonds · protein-protein
- C–D · 4504 Ų buried · 82 hydrogen bonds · protein-protein
- A–C · 754 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6R2D · 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 6R2D · PDBe 6R2D · UniProt A0R2B1
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