SMTL ID : 8td7.1

Structure of PYCR1 complexed with 2S-hydroxy-3-methylbutyric acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-10-mer

Ligands

10 x LHV: (2S)-2-hydroxy-3-methylbutanoic acid(Non-covalent)

LHV.1: 10 residues within 4Å: Chain A: V.253, S.255, G.258, A.259, T.260 Chain B: A.119, M.143, T.193, G.197, S.198 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.253, A:S.255, A:S.255, A:A.259, A:T.260, A:T.260, A:T.260 Hydrophobic interactions: B:A.119, B:T.193 LHV.3: 9 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 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.253, B:S.255, B:A.259, B:T.260, B:T.260 Hydrophobic interactions: A:A.119 LHV.5: 10 residues within 4Å: Chain C: V.253, S.255, G.258, A.259, T.260 Chain D: A.119, M.143, T.193, G.197, S.198 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:V.253, C:V.253, C:S.255, C:A.259, C:T.260, C:T.260 Hydrophobic interactions: D:A.119, D:T.193 LHV.7: 7 residues within 4Å: Chain C: T.193, G.197, S.198 Chain D: V.253, S.255, A.259, T.260 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:V.253, D:S.255, D:S.255, D:A.259, D:T.260, D:T.260 Water bridges: D:S.255 Hydrophobic interactions: C:T.193 LHV.10: 8 residues within 4Å: Chain E: V.253, S.255, A.259, T.260 Chain J: A.119, T.193, G.197, S.198 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain J Hydrogen bonds: E:V.253, E:S.255, E:S.255, E:A.259, E:T.260, E:T.260, E:T.260 Hydrophobic interactions: J:A.119, J:T.193 LHV.12: 10 residues within 4Å: Chain F: V.253, S.255, G.258, A.259, T.260 Chain G: A.119, M.143, T.193, G.197, S.198 9 PLIP interactions: 2 interactions with chain G, 7 interactions with chain F Hydrophobic interactions: G:A.119, G:T.193 Hydrogen bonds: F:V.253, F:S.255, F:S.255, F:A.259, F:T.260, F:T.260, F:T.260 LHV.14: 9 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 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:V.253, G:S.255, G:A.259, G:T.260, G:T.260 Hydrophobic interactions: F:A.119 LHV.16: 10 residues within 4Å: Chain H: V.253, S.255, G.258, A.259, T.260 Chain I: A.119, M.143, T.193, G.197, S.198 8 PLIP interactions: 2 interactions with chain I, 6 interactions with chain H Hydrophobic interactions: I:A.119, I:T.193 Hydrogen bonds: H:V.253, H:V.253, H:S.255, H:A.259, H:T.260, H:T.260 LHV.18: 7 residues within 4Å: Chain H: T.193, G.197, S.198 Chain I: V.253, S.255, A.259, T.260 8 PLIP interactions: 7 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:V.253, I:S.255, I:S.255, I:A.259, I:T.260, I:T.260 Water bridges: I:S.255 Hydrophobic interactions: H:T.193 LHV.21: 8 residues within 4Å: Chain E: A.119, T.193, G.197, S.198 Chain J: V.253, S.255, A.259, T.260 9 PLIP interactions: 2 interactions with chain E, 7 interactions with chain J Hydrophobic interactions: E:A.119, E:T.193 Hydrogen bonds: J:V.253, J:S.255, J:S.255, J:A.259, J:T.260, J:T.260, J:T.260

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

SO4.2: 4 residues within 4Å: Chain A: Q.32, L.61, A.62, T.63 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.32, A:A.62, A:T.63 Water bridges: A:T.63 SO4.4: 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 SO4.6: 3 residues within 4Å: Chain C: G.31, Q.32, L.33 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.32, C:Q.32, C:L.33 Water bridges: C:G.31 SO4.9: 4 residues within 4Å: Chain A: R.222 Chain D: L.61, A.62, T.63 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.62, D:T.63 Water bridges: D:Q.32, D:Q.32 SO4.11: 4 residues within 4Å: Chain E: G.31, Q.32, L.33, K.93 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.32, E:L.33 Water bridges: E:A.34 Salt bridges: E:K.93 SO4.13: 4 residues within 4Å: Chain F: Q.32, L.61, A.62, T.63 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.32, F:A.62, F:T.63 SO4.15: 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 SO4.17: 3 residues within 4Å: Chain H: G.31, Q.32, L.33 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:Q.32, H:Q.32, H:L.33 Water bridges: H:G.31 SO4.20: 4 residues within 4Å: Chain F: R.222 Chain I: L.61, A.62, T.63 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:A.62, I:T.63 Water bridges: I:Q.32, I:Q.32 SO4.22: 4 residues within 4Å: Chain J: G.31, Q.32, L.33, K.93 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:Q.32, J:L.33 Water bridges: J:A.34 Salt bridges: J:K.93

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

PEG.8: 5 residues within 4Å: Chain D: Q.248, D.251, N.252 Chain H: R.221, R.222 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain H Hydrogen bonds: D:Q.248 Water bridges: H:R.221 PEG.19: 5 residues within 4Å: Chain C: R.221, R.222 Chain I: Q.248, D.251, N.252 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain I Water bridges: C:R.221 Hydrogen bonds: I:Q.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meeks, K.R. et al., Screening a knowledge-based library of low molecular weight compounds against the proline biosynthetic enzyme 1-pyrroline-5-carboxylate 1 (PYCR1). Protein Sci. (2024)

Release Date

2024-07-03

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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