Research workbench
Crystal structure of medicago truncatula (DELTA)1-pyrroline-5- carboxylate reductase (MTP5CR) in complex with NAD+
Analyse Crystal structure of medicago truncatula (DELTA)1-pyrroline-5- carboxylate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BSF
- Type
- protein
- Length
- 2,713 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrroline-5-carboxylate reductase
- EC
- 1.5.1.2
- UniProt
- G7KRM5
- Ligands
- NAD, CL
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, H, I, J | Pyrroline-5-carboxylate reductase (EC 1.5.1.2) | protein | 272 | 57% helix, 13% strand | G7KRM5 |
| C | Pyrroline-5-carboxylate reductase (EC 1.5.1.2) | protein | 270 | 57% helix, 13% strand | G7KRM5 |
| D | Pyrroline-5-carboxylate reductase (EC 1.5.1.2) | protein | 271 | 57% helix, 13% strand | G7KRM5 |
| G | Pyrroline-5-carboxylate reductase (EC 1.5.1.2) | protein | 268 | 59% helix, 13% strand | G7KRM5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- CL · Chloride ion · ion · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.71 | 0.78 | 56 | CL, NAD, MPO |
| 2 | 714 | 0.71 | 0.78 | 60 | NAD, MPO, CL |
| 3 | 658 | 0.71 | 0.78 | 53 | NAD, MPO, CL |
| 4 | 671 | 0.71 | 0.78 | 62 | NAD, MPO, CL |
| 5 | 640 | 0.70 | 0.78 | 61 | CL, NAD, MPO |
Interfaces
25 interfaces between chains.
- G–H · 4208 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 4206 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 4188 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 4186 Ų buried · 16 hydrogen bonds · protein-protein
- I–J · 4169 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5BSF · Crystal structure of Medicago truncatula (delta)1-Pyrroline-5-Carboxylate Reductase… · 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 G7KRM5
- Elsewhere: RCSB PDB 5BSF · PDBe 5BSF · UniProt G7KRM5
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