Research workbench
Mycobacterium tuberculosis thyx-NADP complex
Analyse Mycobacterium tuberculosis thyx-NADP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GQ2
- Type
- protein
- Length
- 919 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase thyx
- EC
- 2.1.1.148
- UniProt
- P66930
- Ligands
- NAP, K, IOD
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 242 | 47% helix, 20% strand | P66930 |
| B | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 226 | 46% helix, 20% strand | P66930 |
| C | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 225 | 46% helix, 20% strand | P66930 |
| D | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 226 | 48% helix, 20% strand | P66930 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, C, D, B
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- IOD · Iodide ion · ion · 15 copies · chains A, D, B, C
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.86 | 0.88 | 93 | K, NAP, IOD |
| 2 | 340 | 0.78 | 0.89 | 56 | PGE, NAP |
| 3 | 334 | 0.75 | 0.87 | 51 | IOD, NAP |
| 4 | 240 | 0.71 | 0.87 | 32 | NAP |
| 5 | 60 | 0.69 | 0.96 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1714 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1692 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1642 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1631 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 241 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 2GQ2 · Mycobacterium tuberculosis ThyX-NADP complex · 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 P66930
- Elsewhere: RCSB PDB 2GQ2 · PDBe 2GQ2 · UniProt P66930
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