SMTL ID : 6xp3.1

Structure of human PYCR1 complexed with cyclopentanecarboxylic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-10-mer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: V.253, S.254, S.255, G.258, A.259, T.260 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.255, A:S.255, A:S.255, A:A.259, A:T.260, A:T.260 Water bridges: A:I.261 SO4.3: 3 residues within 4Å: Chain B: S.242, E.243, Q.244 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.241, B:E.243, B:Q.244 SO4.5: 6 residues within 4Å: Chain D: V.253, S.254, S.255, G.258, A.259, T.260 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.255, D:A.259, D:T.260, D:T.260 Water bridges: D:I.261 SO4.6: 6 residues within 4Å: Chain E: V.253, S.254, S.255, G.258, A.259, T.260 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:S.255, E:S.255, E:A.259, E:T.260, E:T.260 Water bridges: E:S.255, E:S.255, E:I.261 SO4.7: 6 residues within 4Å: Chain F: V.253, S.254, S.255, G.258, A.259, T.260 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:S.255, F:S.255, F:S.255, F:A.259, F:T.260 Water bridges: F:I.261 SO4.9: 3 residues within 4Å: Chain G: S.242, E.243, Q.244 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:H.241, G:E.243, G:Q.244 SO4.11: 6 residues within 4Å: Chain I: V.253, S.254, S.255, G.258, A.259, T.260 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:S.255, I:A.259, I:T.260, I:T.260, I:T.260 Water bridges: I:I.261 SO4.12: 6 residues within 4Å: Chain J: V.253, S.254, S.255, G.258, A.259, T.260 8 PLIP interactions: 8 interactions with chain J Hydrogen bonds: J:S.255, J:S.255, J:A.259, J:T.260, J:T.260 Water bridges: J:S.255, J:S.255, J:I.261

4 x IQ0: cyclopentanecarboxylic acid(Non-covalent)

IQ0.2: 9 residues within 4Å: Chain A: A.119, T.193, G.197, S.198 Chain B: V.253, S.255, G.258, A.259, T.260 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.255, B:A.259, B:T.260 Water bridges: B:G.258 Hydrophobic interactions: A:A.119, A:T.193 IQ0.4: 9 residues within 4Å: Chain C: V.253, S.255, G.258, A.259, T.260 Chain D: A.119, T.193, G.197, S.198 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.255, C:A.259, C:T.260, C:T.260, C:T.260 Hydrophobic interactions: D:A.119, D:T.193 IQ0.8: 9 residues within 4Å: Chain F: A.119, T.193, G.197, S.198 Chain G: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 5 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:S.255, G:A.259, G:T.260, G:T.260 Water bridges: G:G.258 Hydrophobic interactions: F:A.119, F:T.193 IQ0.10: 9 residues within 4Å: Chain H: V.253, S.255, G.258, A.259, T.260 Chain I: A.119, T.193, G.197, S.198 6 PLIP interactions: 4 interactions with chain H, 2 interactions with chain I Hydrogen bonds: H:S.255, H:A.259, H:T.260, H:T.260 Hydrophobic interactions: I:A.119, I:T.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Christensen, E.M. et al., In crystallo screening for proline analog inhibitors of the proline cycle enzyme PYCR1. J.Biol.Chem. (2020)

Release Date

2020-11-04

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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