SMTL ID : 5uav.1 (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-10-mer

Ligands

10 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, 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: N.252, V.253 Ligands: TFB.4 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.33 Hydrogen bonds: A:A.30, A:A.30, A:Q.32, A:L.33, A:D.58, A:N.78, A:V.92, A:A.119, B:N.252 Water bridges: A:G.31, A:A.34, A:T.146 Salt bridges: A:K.93, A:K.93 NDP.3: 25 residues within 4Å: 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 Hydrogen bonds: B:A.30, B:A.30, B:Q.32, B:L.33, B:S.56, B:D.58, B:N.78, B:V.92, B:A.119 Water bridges: B:G.31, B:Q.32, B:A.34, B:K.93, B:K.93, B:T.146, A:T.260 Salt bridges: B:K.93, B:K.93 NDP.5: 27 residues within 4Å: Chain C: 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 D: V.253 Ligands: TFB.9 20 PLIP interactions: 2 interactions with chain D, 18 interactions with chain C Hydrogen bonds: D:V.253, C:A.30, C:A.30, C:Q.32, C:L.33, C:S.56, C:S.56, C:D.58, C:N.78, C:V.92, C:A.119 Water bridges: D:T.260, C:G.31, C:Q.32, C:A.34, C:D.58, C:D.58 Hydrophobic interactions: C:L.33 Salt bridges: C:K.93, C:K.93 NDP.8: 26 residues within 4Å: Chain C: V.253 Chain D: 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.6 18 PLIP interactions: 17 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.33 Hydrogen bonds: D:A.30, D:A.30, D:Q.32, D:L.33, D:D.58, D:N.78, D:V.92, D:A.119, C:N.252 Water bridges: D:G.31, D:A.34, D:N.78, D:K.93, D:K.93, D:T.146 Salt bridges: D:K.93, D:K.93 NDP.10: 28 residues within 4Å: Chain E: 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 J: N.252, V.253 Ligands: TFB.11 15 PLIP interactions: 14 interactions with chain E, 1 interactions with chain J Hydrophobic interactions: E:L.33 Hydrogen bonds: E:A.30, E:A.30, E:Q.32, E:L.33, E:S.56, E:S.56, E:D.58, E:N.78, E:V.92, E:A.119, J:N.252 Water bridges: E:G.31, E:A.34 Salt bridges: E:K.93 NDP.12: 27 residues within 4Å: Chain F: 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 Chain G: N.252, V.253 Ligands: TFB.15 15 PLIP interactions: 14 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:L.33 Hydrogen bonds: F:A.30, F:A.30, F:Q.32, F:L.33, F:D.58, F:N.78, F:V.92, F:A.119, G:N.252 Water bridges: F:G.31, F:A.34, F:T.146 Salt bridges: F:K.93, F:K.93 NDP.14: 25 residues within 4Å: Chain G: 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.13 18 PLIP interactions: 17 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:A.30, G:A.30, G:Q.32, G:L.33, G:S.56, G:D.58, G:N.78, G:V.92, G:A.119 Water bridges: G:G.31, G:Q.32, G:A.34, G:K.93, G:K.93, G:T.146, F:T.260 Salt bridges: G:K.93, G:K.93 NDP.16: 27 residues within 4Å: Chain H: 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 I: V.253 Ligands: TFB.20 20 PLIP interactions: 2 interactions with chain I, 18 interactions with chain H Hydrogen bonds: I:V.253, H:A.30, H:A.30, H:Q.32, H:L.33, H:S.56, H:S.56, H:D.58, H:N.78, H:V.92, H:A.119 Water bridges: I:T.260, H:G.31, H:Q.32, H:A.34, H:D.58, H:D.58 Hydrophobic interactions: H:L.33 Salt bridges: H:K.93, H:K.93 NDP.19: 26 residues within 4Å: Chain H: V.253 Chain I: 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.17 18 PLIP interactions: 17 interactions with chain I, 1 interactions with chain H Hydrophobic interactions: I:L.33 Hydrogen bonds: I:A.30, I:A.30, I:Q.32, I:L.33, I:D.58, I:N.78, I:V.92, I:A.119, H:N.252 Water bridges: I:G.31, I:A.34, I:N.78, I:K.93, I:K.93, I:T.146 Salt bridges: I:K.93, I:K.93 NDP.21: 28 residues within 4Å: Chain E: N.252, V.253 Chain J: 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 Ligands: TFB.22 15 PLIP interactions: 14 interactions with chain J, 1 interactions with chain E Hydrophobic interactions: J:L.33 Hydrogen bonds: J:A.30, J:A.30, J:Q.32, J:L.33, J:S.56, J:S.56, J:D.58, J:N.78, J:V.92, J:A.119, E:N.252 Water bridges: J:G.31, J:A.34 Salt bridges: J:K.93

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

TFB.2: 9 residues within 4Å: Chain A: S.255, G.258, A.259, T.260 Chain B: A.119, T.193, G.197, S.198 Ligands: NDP.3 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.259, A:T.260, A:T.260, A:T.260 Water bridges: A:S.255, A:S.255, A:S.255 Hydrophobic interactions: B:A.119, B:T.193 TFB.4: 10 residues within 4Å: Chain A: A.119, M.143, T.193, G.197, S.198 Chain B: V.253, S.255, A.259, T.260 Ligands: NDP.1 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.119, A:T.193 Hydrogen bonds: B:S.255, B:A.259, B:T.260, B:T.260, B:T.260 Water bridges: B:S.255 TFB.6: 9 residues within 4Å: Chain C: V.253, S.255, G.258, A.259, T.260 Chain D: A.119, T.193, G.197 Ligands: NDP.8 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:V.253, C:S.255, C:A.259, C:T.260, C:T.260 Water bridges: C:S.255, C:G.258 Hydrophobic interactions: D:A.119, D:T.193 TFB.9: 10 residues within 4Å: Chain C: A.119, T.193, G.197, S.198, L.290 Chain D: S.255, G.258, A.259, T.260 Ligands: NDP.5 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.255, D:A.259, D:T.260, D:T.260 Water bridges: D:S.255, D:I.261 Hydrophobic interactions: C:A.119, C:T.193 TFB.11: 9 residues within 4Å: Chain E: A.119, T.193, G.197 Chain J: V.253, S.255, G.258, A.259, T.260 Ligands: NDP.10 8 PLIP interactions: 2 interactions with chain E, 6 interactions with chain J Hydrophobic interactions: E:A.119, E:T.193 Hydrogen bonds: J:S.255, J:A.259, J:T.260, J:T.260 Water bridges: J:S.255, J:S.255 TFB.13: 9 residues within 4Å: Chain F: S.255, G.258, A.259, T.260 Chain G: A.119, T.193, G.197, S.198 Ligands: NDP.14 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:A.259, F:T.260, F:T.260, F:T.260 Water bridges: F:S.255, F:S.255, F:S.255 Hydrophobic interactions: G:A.119, G:T.193 TFB.15: 10 residues within 4Å: Chain F: A.119, M.143, T.193, G.197, S.198 Chain G: V.253, S.255, A.259, T.260 Ligands: NDP.12 8 PLIP interactions: 2 interactions with chain F, 6 interactions with chain G Hydrophobic interactions: F:A.119, F:T.193 Hydrogen bonds: G:S.255, G:A.259, G:T.260, G:T.260, G:T.260 Water bridges: G:S.255 TFB.17: 9 residues within 4Å: Chain H: V.253, S.255, G.258, A.259, T.260 Chain I: A.119, T.193, G.197 Ligands: NDP.19 9 PLIP interactions: 7 interactions with chain H, 2 interactions with chain I Hydrogen bonds: H:V.253, H:S.255, H:A.259, H:T.260, H:T.260 Water bridges: H:S.255, H:G.258 Hydrophobic interactions: I:A.119, I:T.193 TFB.20: 10 residues within 4Å: Chain H: A.119, T.193, G.197, S.198, L.290 Chain I: S.255, G.258, A.259, T.260 Ligands: NDP.16 8 PLIP interactions: 6 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:S.255, I:A.259, I:T.260, I:T.260 Water bridges: I:S.255, I:I.261 Hydrophobic interactions: H:A.119, H:T.193 TFB.22: 9 residues within 4Å: Chain E: V.253, S.255, G.258, A.259, T.260 Chain J: A.119, T.193, G.197 Ligands: NDP.21 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain J Hydrogen bonds: E:S.255, E:A.259, E:T.260, E:T.260 Water bridges: E:S.255, E:S.255 Hydrophobic interactions: J:A.119, J:T.193

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

PEG.7: 1 residues within 4Å: Chain C: L.61 No protein-ligand interaction detected (PLIP) PEG.18: 1 residues within 4Å: Chain H: 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: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

Pyrroline-5-carboxylate reductase 1, mitochondrial

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