Research workbench
Cryptococcus neoformans thymidylate synthase complexed with substrate and an antifolate
Analyse Cryptococcus neoformans thymidylate synthase complexed with substrate and an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AAZ
- Type
- protein
- Length
- 4,832 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P45351
- Ligands
- UMP, CB3
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Thymidylate synthase (EC 2.1.1.45) | protein | 305 | 33% helix, 21% strand | P45351 |
| I, J, K, L, M, N, O, P | Thymidylate synthase (EC 2.1.1.45) | protein | 299 | 34% helix, 21% strand | P45351 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- CB3 · 10-propargyl-5,8-dideazafolic acid · ligand · 8 copies · chains A, B, C, F, D, E, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.86 | 0.87 | 102 | UMP |
| 2 | 1176 | 0.86 | 0.87 | 106 | UMP, CB3 |
| 3 | 833 | 0.85 | 0.87 | 89 | UMP, CB3 |
| 4 | 764 | 0.84 | 0.87 | 77 | UMP, CB3 |
| 5 | 1114 | 0.84 | 0.85 | 105 | empty |
Interfaces
19 interfaces between chains.
- A–B · 2128 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 2126 Ų buried · 27 hydrogen bonds · protein-protein
- K–L · 2122 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2122 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2119 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent (covalent ligand).
Compared structures
- 2AAZ · Cryptococcus neoformans thymidylate synthase complexed with substrate and an antifolate · the same entry in another collection · chain B against B, 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 P45351
- Elsewhere: RCSB PDB 2AAZ · PDBe 2AAZ · UniProt P45351
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