SMTL ID : 6xoz.1

Structure of human PYCR1 complexed with L-tetrahydro-2-furoic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-10-mer

Ligands

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

TFB.1: 7 residues within 4Å: Chain A: V.253, S.255, G.258, A.259, T.260 Chain B: T.193, G.197 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.255, A:S.255, A:A.259, A:T.260, A:T.260 Water bridges: A:S.255, A:G.258 Hydrophobic interactions: B:T.193 TFB.3: 6 residues within 4Å: Chain A: G.197 Chain B: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:V.253, B:S.255, B:A.259, B:T.260, B:T.260 Water bridges: B:S.255, B:G.258 TFB.4: 7 residues within 4Å: Chain C: V.253, S.255, G.258, A.259, T.260 Chain D: T.193, G.197 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.255, C:S.255, C:A.259, C:T.260, C:T.260 Water bridges: C:S.255 Hydrophobic interactions: D:T.193 TFB.5: 10 residues within 4Å: Chain C: A.119, M.143, T.193, G.197, S.198 Chain D: V.253, S.255, G.258, A.259, T.260 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:A.119, C:T.193 Hydrogen bonds: D:V.253, D:S.255, D:A.259, D:T.260, D:T.260 Water bridges: D:S.255, D:G.258 TFB.6: 9 residues within 4Å: Chain E: V.253, S.254, S.255, G.258, A.259, T.260 Chain J: T.193, G.197, S.198 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain J Hydrogen bonds: E:S.255, E:A.259, E:T.260, E:T.260 Water bridges: E:G.258 Hydrophobic interactions: J:T.193 TFB.7: 7 residues within 4Å: Chain F: V.253, S.255, G.258, A.259, T.260 Chain G: T.193, G.197 8 PLIP interactions: 1 interactions with chain G, 7 interactions with chain F Hydrophobic interactions: G:T.193 Hydrogen bonds: F:S.255, F:S.255, F:A.259, F:T.260, F:T.260 Water bridges: F:S.255, F:G.258 TFB.9: 6 residues within 4Å: Chain F: G.197 Chain G: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:V.253, G:S.255, G:A.259, G:T.260 Water bridges: G:S.255, G:G.258, G:T.260 TFB.10: 7 residues within 4Å: Chain H: V.253, S.255, G.258, A.259, T.260 Chain I: T.193, G.197 7 PLIP interactions: 1 interactions with chain I, 6 interactions with chain H Hydrophobic interactions: I:T.193 Hydrogen bonds: H:S.255, H:S.255, H:A.259, H:T.260, H:T.260 Water bridges: H:S.255 TFB.11: 10 residues within 4Å: Chain H: A.119, M.143, T.193, G.197, S.198 Chain I: V.253, S.255, G.258, A.259, T.260 9 PLIP interactions: 2 interactions with chain H, 7 interactions with chain I Hydrophobic interactions: H:A.119, H:T.193 Hydrogen bonds: I:V.253, I:S.255, I:A.259, I:T.260, I:T.260 Water bridges: I:S.255, I:G.258 TFB.12: 9 residues within 4Å: Chain E: T.193, G.197, S.198 Chain J: V.253, S.254, S.255, G.258, A.259, T.260 6 PLIP interactions: 5 interactions with chain J, 1 interactions with chain E Hydrogen bonds: J:S.255, J:A.259, J:T.260, J:T.260 Water bridges: J:G.258 Hydrophobic interactions: E:T.193

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: N.145, T.146, P.147, P.200 Chain B: V.253 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain F: N.145, T.146, P.147, P.200 Chain G: V.253 Ligand excluded by PLIP

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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