MolNFT v1 · #114535 · protein

Crystal structure of medicago truncatula (DELTA)1-pyrroline-5- carboxylate reductase (MTP5CR) in complex with NAD+

5BSF · Pyrroline-5-carboxylate reductase: “Crystal structure of medicago truncatula (DELTA)1-pyrroline-5- carboxylate reductase (MTP5CR) in complex with…”. X-ray diffraction, 2 ligands (NAD, CL), 20 pockets (best druggability 0.71). MolNFT…

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.

Pocket	Volume (Å³)	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 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 4206 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 4188 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 4186 Å² buried · 16 hydrogen bonds · protein-protein
I–J · 4169 Å² 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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