Research workbench
Crystal structure of W139G D-3-phosphoglycerate dehydrogenase complexed with NAD+
Analyse Crystal structure of W139G D-3-phosphoglycerate dehydrogenase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SC6
- Type
- protein
- Length
- 1,537 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-3-phosphoglycerate dehydrogenase
- EC
- 1.1.1.95
- UniProt
- P0A9T0
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) | protein | 390 | 35% helix, 22% strand | P0A9T0 |
| B | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) | protein | 385 | 34% helix, 21% strand | P0A9T0 |
| C | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) | protein | 378 | 34% helix, 22% strand | P0A9T0 |
| D | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) | protein | 384 | 34% helix, 22% strand | P0A9T0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.82 | 0.91 | 69 | empty |
| 2 | 942 | 0.76 | 0.79 | 107 | empty |
| 3 | 644 | 0.75 | 0.81 | 93 | empty |
| 4 | 87 | 0.60 | 0.88 | 19 | empty |
| 5 | 251 | 0.57 | 0.78 | 27 | NAD |
Interfaces
6 interfaces between chains.
- A–B · 1932 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1711 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1671 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1558 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 302 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 1SC6 · Crystal Structure of W139G D-3-Phosphoglycerate dehydrogenase complexed with NAD+ · the same entry in another collection · chain D against D, TM-score 1.00
- P0A9T0 · AlphaFold monomer V2.0 prediction for D-3-phosphoglycerate dehydrogenase (P0A9T0) · a predicted model of the same protein · chain D against A, TM-score 0.84
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 P0A9T0
- Elsewhere: RCSB PDB 1SC6 · PDBe 1SC6 · UniProt P0A9T0
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