Research workbench
Pteridine reductase from leishmania tarentolae complex with NADPH and mtx
Analyse Pteridine reductase from leishmania tarentolae complex with NADPH and mtx in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P33
- Type
- protein
- Length
- 1,072 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase 1
- EC
- 1.1.1.253
- UniProt
- P42556
- Ligands
- NDP, MTX
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pteridine reductase 1 (EC 1.1.1.253) | protein | 267 | 45% helix, 15% strand | P42556 |
| B | Pteridine reductase 1 (EC 1.1.1.253) | protein | 269 | 45% helix, 14% strand | P42556 |
| C | Pteridine reductase 1 (EC 1.1.1.253) | protein | 268 | 45% helix, 15% strand | P42556 |
| D | Pteridine reductase 1 (EC 1.1.1.253) | protein | 268 | 45% helix, 13% strand | P42556 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- MTX · Methotrexate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.82 | 0.84 | 71 | empty |
| 2 | 632 | 0.77 | 0.83 | 44 | NDP, MTX |
| 3 | 575 | 0.77 | 0.83 | 47 | NDP, MTX |
| 4 | 600 | 0.75 | 0.82 | 45 | NDP, MTX |
| 5 | 593 | 0.74 | 0.81 | 47 | NDP, MTX |
Interfaces
6 interfaces between chains.
- A–C · 2083 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 2003 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1592 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1578 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 641 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1P33 · Pteridine reductase from Leishmania tarentolae complex with NADPH and MTX · the same entry in another collection · chain D against D, TM-score 1.00
- P42556 · AlphaFold monomer V2.0 prediction for pteridine reductase 1 (P42556) · 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 P42556
- Elsewhere: RCSB PDB 1P33 · PDBe 1P33 · UniProt P42556
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