MolNFT v1 · #168447 · protein
Crystal structure of a putative citrate synthase 2 from mycobacterium bovis in complex with citrate
6WGY: “Crystal structure of a putative citrate synthase 2 from mycobacterium bovis in complex with citrate”. X-ray diffraction, 1 ligand (IOD), 13 pockets (best druggability 0.89). MolNFT v1 #168447 on GenesisL1: 3D structure, binding…
- PDB
- 6WGY
- Type
- protein
- Length
- 1,492 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative citrate synthase 2
- EC
- 2.3.3.16
- UniProt
- P63778
- Ligands
- IOD
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative citrate synthase 2 (EC 2.3.3.16) | protein | 374 | 55% helix, 7% strand | P63778 |
| C | Putative citrate synthase 2 (EC 2.3.3.16) | protein | 371 | 54% helix, 7% strand | P63778 |
| D | Putative citrate synthase 2 (EC 2.3.3.16) | protein | 373 | 54% helix, 7% strand | P63778 |
Ligands and binding sites
- IOD · Iodide ion · ion · 109 copies · chains A, D, C, B
- CIT · Citric acid · additive · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.89 | 0.90 | 140 | IOD |
| 2 | 621 | 0.68 | 0.77 | 83 | IOD |
| 3 | 237 | 0.56 | 0.79 | 34 | IOD, CIT |
| 4 | 167 | 0.56 | 0.81 | 24 | IOD, CIT |
| 5 | 288 | 0.55 | 0.76 | 42 | IOD |
Interfaces
6 interfaces between chains.
- A–D · 4250 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 4111 Ų buried · 52 hydrogen bonds · protein-protein
- B–D · 392 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 385 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 325 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6WGY · Crystal structure of a Putative citrate synthase 2 from Mycobacterium bovis in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- P63778 · AlphaFold monomer V2.0 prediction for putative citrate synthase 2 (P63778) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P63778
- Elsewhere: RCSB PDB 6WGY · PDBe 6WGY · UniProt P63778
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