SMTL ID : 5uav.3 (3 other biounits)

Structure of human PYCR-1 complexed with NADPH and L-tetrahydrofuroic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 27 residues within 4Å: Chain A: I.28, G.29, A.30, G.31, Q.32, L.33, S.55, S.56, P.57, D.58, M.59, N.78, A.91, V.92, K.93, P.94, I.96, I.100, C.117, A.118, A.119, M.143, T.144, N.145, T.146 Chain B: V.253 Ligands: TFB.5 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.33 Hydrogen bonds: A:A.30, A:A.30, A:Q.32, A:L.33, A:S.56, A:S.56, A:D.58, A:N.78, A:V.92, A:A.119, B:V.253 Water bridges: A:G.31, A:Q.32, A:A.34, A:D.58, A:D.58, B:T.260 Salt bridges: A:K.93, A:K.93 NDP.4: 26 residues within 4Å: Chain A: V.253 Chain B: I.28, G.29, A.30, G.31, Q.32, L.33, S.55, S.56, P.57, D.58, N.78, A.91, V.92, K.93, P.94, I.96, I.100, C.117, A.118, A.119, M.143, T.144, N.145, T.146 Ligands: TFB.2 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.33 Hydrogen bonds: B:A.30, B:A.30, B:Q.32, B:L.33, B:D.58, B:N.78, B:V.92, B:A.119, A:N.252 Water bridges: B:G.31, B:A.34, B:N.78, B:K.93, B:K.93, B:T.146 Salt bridges: B:K.93, B:K.93

2 x TFB: TETRAHYDROFURAN-2-CARBOXYLIC ACID(Non-covalent)

TFB.2: 9 residues within 4Å: Chain A: V.253, S.255, G.258, A.259, T.260 Chain B: A.119, T.193, G.197 Ligands: NDP.4 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.253, A:S.255, A:A.259, A:T.260, A:T.260 Water bridges: A:S.255, A:G.258 Hydrophobic interactions: B:A.119, B:T.193 TFB.5: 10 residues within 4Å: Chain A: A.119, T.193, G.197, S.198, L.290 Chain B: S.255, G.258, A.259, T.260 Ligands: NDP.1 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.255, B:A.259, B:T.260, B:T.260 Water bridges: B:S.255, B:I.261 Hydrophobic interactions: A:A.119, A:T.193

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 1 residues within 4Å: Chain A: L.61 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Christensen, E.M. et al., Resolving the cofactor-binding site in the proline biosynthetic enzyme human pyrroline-5-carboxylate reductase 1. J. Biol. Chem. (2017)

Release Date

2017-03-15

Peptides

Pyrroline-5-carboxylate reductase 1, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Pyrroline-5-carboxylate reductase 1, mitochondrial

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