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Structure of an N-terminal nucleophile (ntn) hydrolase, OAT2, in complex with glutamate
Analyse Structure of an N-terminal nucleophile (ntn) hydrolase, OAT2, in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YEP
- Type
- protein
- Length
- 1,507 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate N-acetyltransferase 2 alpha chain; Glutamate N-acetyltransferase 2 beta chain
- EC
- 2.3.1.35
- UniProt
- Q53940
- Ligands
- GLU
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Glutamate N-acetyltransferase 2 alpha chain (EC 2.3.1.35) | protein | 173 | 28% helix, 26% strand | Q53940 |
| B | Glutamate N-acetyltransferase 2 beta chain (EC 2.3.1.35) | protein | 213 | 41% helix, 25% strand | Q53940 |
| D | Glutamate N-acetyltransferase 2 beta chain (EC 2.3.1.35) | protein | 210 | 43% helix, 22% strand | Q53940 |
| F | Glutamate N-acetyltransferase 2 beta chain (EC 2.3.1.35) | protein | 197 | 41% helix, 24% strand | Q53940 |
| H | Glutamate N-acetyltransferase 2 beta chain (EC 2.3.1.35) | protein | 195 | 39% helix, 24% strand | Q53940 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 760 | 0.77 | 0.81 | 98 | GLU |
| 2 | 1087 | 0.74 | 0.77 | 96 | ACT |
| 3 | 173 | 0.56 | 0.81 | 24 | empty |
| 4 | 251 | 0.55 | 0.77 | 42 | empty |
| 5 | 195 | 0.48 | 0.76 | 31 | empty |
Interfaces
18 interfaces between chains.
- A–B · 2705 Ų buried · 62 hydrogen bonds · protein-protein
- E–F · 2654 Ų buried · 60 hydrogen bonds · protein-protein
- C–D · 2616 Ų buried · 59 hydrogen bonds · protein-protein
- G–H · 2590 Ų buried · 59 hydrogen bonds · protein-protein
- C–E · 444 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 2YEP · Structure of an N-terminal nucleophile (ntn) hydrolase, OAT2, in complex with glutamate · the same entry in another collection · chain H against H, 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 Q53940
- Elsewhere: RCSB PDB 2YEP · PDBe 2YEP · UniProt Q53940
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