SMTL ID : 5uat.1 (3 other biounits)

Structure of human PYCR-1 complexed with NADPH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-10-mer

Ligands

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: V.253, S.255, G.258, A.259, T.260 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.255, A:S.255, A:T.260 Water bridges: A:A.259, A:A.259, A:T.260, A:T.260, A:I.261 SO4.2: 6 residues within 4Å: Chain A: A.119 Chain B: V.253, S.255, G.258, A.259, T.260 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.255, B:S.255, B:S.255, B:T.260 Water bridges: B:A.259, B:T.260, B:T.260, B:I.261 SO4.4: 5 residues within 4Å: Chain C: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:V.253, C:S.255, C:S.255, C:A.259, C:T.260, C:T.260 Water bridges: C:G.258 SO4.6: 6 residues within 4Å: Chain D: V.253, S.255, G.258, A.259, T.260 Ligands: NDP.3 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.255, D:A.259, D:T.260, D:T.260, D:T.260 SO4.8: 5 residues within 4Å: Chain F: V.253, S.255, G.258, A.259, T.260 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:S.255, F:S.255, F:T.260 Water bridges: F:A.259, F:A.259, F:T.260, F:T.260, F:I.261 SO4.9: 6 residues within 4Å: Chain F: A.119 Chain G: V.253, S.255, G.258, A.259, T.260 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:S.255, G:S.255, G:S.255, G:T.260 Water bridges: G:A.259, G:T.260, G:T.260, G:I.261 SO4.11: 5 residues within 4Å: Chain H: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:V.253, H:S.255, H:S.255, H:A.259, H:T.260, H:T.260 Water bridges: H:G.258 SO4.13: 6 residues within 4Å: Chain I: V.253, S.255, G.258, A.259, T.260 Ligands: NDP.10 5 PLIP interactions: 5 interactions with chain I Hydrogen bonds: I:S.255, I:A.259, I:T.260, I:T.260, I:T.260

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

NDP.3: 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, T.146 Chain D: N.252, V.253 Ligands: SO4.6 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain D Hydrogen bonds: 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, D:N.252 Water bridges: C:G.31, C:A.34, C:D.58, C:E.103, C:T.146 NDP.7: 26 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, T.146 Chain J: N.252, V.253 14 PLIP interactions: 13 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 NDP.10: 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, T.146 Chain I: N.252, V.253 Ligands: SO4.13 16 PLIP interactions: 15 interactions with chain H, 1 interactions with chain I Hydrogen bonds: 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, I:N.252 Water bridges: H:G.31, H:A.34, H:D.58, H:E.103, H:T.146 NDP.14: 26 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, T.146 14 PLIP interactions: 13 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

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

PEG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.12: 0 residues within 4Å: (No contacts) 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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