Research workbench
Anthranilate phosphoribosyl-transferase (trpd) from S. solfataricus in complex with anthranilate
Analyse Anthranilate phosphoribosyl-transferase (trpd) from S. solfataricus in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GVQ
- Type
- protein
- Length
- 1,366 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anthranilate phosphoribosyltransferase
- EC
- 2.4.2.18
- UniProt
- P50384
- Ligands
- BE2
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 340 | 53% helix, 13% strand | P50384 |
| C | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 341 | 54% helix, 14% strand | P50384 |
| D | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 345 | 53% helix, 12% strand | P50384 |
Ligands and binding sites
- BE2 · 2-aminobenzoic acid · ligand · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.77 | 0.82 | 72 | BE2 |
| 2 | 728 | 0.75 | 0.81 | 62 | BE2 |
| 3 | 582 | 0.72 | 0.80 | 54 | BE2 |
| 4 | 575 | 0.72 | 0.80 | 47 | BE2 |
| 5 | 75 | 0.42 | 0.80 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–D · 967 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 958 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2GVQ · Anthranilate phosphoribosyl-transferase (TRPD) from S. solfataricus in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- P50384 · AlphaFold monomer V2.0 prediction for anthranilate phosphoribosyltransferase (P50384) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P50384
- Elsewhere: RCSB PDB 2GVQ · PDBe 2GVQ · UniProt P50384
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