SMTL ID : 8td9.1

Structure of PYCR1 complexed with NADH and L-pipecolic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-10-mer

Ligands

10 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.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, L.61, 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: YCP.6 18 PLIP interactions: 12 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:A.30, A:A.30, A:Q.32, A:L.33, A:S.56, A:N.78, A:V.92, A:A.119, B:N.252 Water bridges: A:G.31, A:Q.32, A:A.34, A:T.146, B:N.252, B:S.255, B:S.255, B:S.255, B:S.255 NAI.4: 27 residues within 4Å: Chain A: N.252, V.253 Chain B: I.28, G.29, A.30, G.31, Q.32, L.33, S.55, S.56, P.57, L.61, 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: YCP.3 16 PLIP interactions: 4 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:N.252, B:A.30, B:A.30, B:Q.32, B:L.33, B:S.56, B:N.78, B:V.92, B:A.119 Water bridges: A:N.252, A:S.255, A:S.255, B:G.31, B:A.34, B:T.146 Hydrophobic interactions: B:L.33 NAI.7: 26 residues within 4Å: Chain C: I.28, G.29, A.30, G.31, Q.32, L.33, S.55, S.56, P.57, 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: N.252, V.253 Ligands: YCP.13 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:A.30, C:A.30, C:Q.32, C:L.33, C:S.56, C:N.78, C:V.92, C:A.119, D:N.252 Water bridges: C:G.31, C:A.34, C:N.78, C:K.93, C:K.93, C:T.146, D:N.252, D:S.255 NAI.10: 27 residues within 4Å: Chain C: N.252, V.253 Chain D: I.28, G.29, A.30, G.31, Q.32, L.33, S.55, S.56, P.57, L.61, 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: YCP.9 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:A.30, D:A.30, D:Q.32, D:L.33, D:S.56, D:N.78, D:V.92, D:A.119, C:N.252 Water bridges: D:G.31, D:A.34, D:K.93, D:K.93, D:T.146, C:N.252, C:S.255 NAI.14: 27 residues within 4Å: Chain E: I.28, G.29, A.30, G.31, Q.32, L.33, S.55, S.56, P.57, L.61, 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: YCP.30 15 PLIP interactions: 12 interactions with chain E, 3 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:N.78, E:V.92, E:A.119, J:N.252 Water bridges: E:G.31, E:A.34, E:T.146, J:N.252, J:S.255 NAI.16: 27 residues within 4Å: Chain F: I.28, G.29, A.30, G.31, Q.32, L.33, S.55, S.56, P.57, L.61, 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: YCP.21 18 PLIP interactions: 12 interactions with chain F, 6 interactions with chain G Hydrogen bonds: F:A.30, F:A.30, F:Q.32, F:L.33, F:S.56, F:N.78, F:V.92, F:A.119, G:N.252 Water bridges: F:G.31, F:Q.32, F:A.34, F:T.146, G:N.252, G:S.255, G:S.255, G:S.255, G:S.255 NAI.19: 27 residues within 4Å: Chain F: N.252, V.253 Chain G: I.28, G.29, A.30, G.31, Q.32, L.33, S.55, S.56, P.57, L.61, 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: YCP.18 16 PLIP interactions: 12 interactions with chain G, 4 interactions with chain F Hydrophobic interactions: G:L.33 Hydrogen bonds: G:A.30, G:A.30, G:Q.32, G:L.33, G:S.56, G:N.78, G:V.92, G:A.119, F:N.252 Water bridges: G:G.31, G:A.34, G:T.146, F:N.252, F:S.255, F:S.255 NAI.22: 26 residues within 4Å: Chain H: I.28, G.29, A.30, G.31, Q.32, L.33, S.55, S.56, P.57, 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: N.252, V.253 Ligands: YCP.28 17 PLIP interactions: 14 interactions with chain H, 3 interactions with chain I Hydrogen bonds: H:A.30, H:A.30, H:Q.32, H:L.33, H:S.56, H:N.78, H:V.92, H:A.119, I:N.252 Water bridges: H:G.31, H:A.34, H:N.78, H:K.93, H:K.93, H:T.146, I:N.252, I:S.255 NAI.25: 27 residues within 4Å: Chain H: N.252, V.253 Chain I: I.28, G.29, A.30, G.31, Q.32, L.33, S.55, S.56, P.57, L.61, 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: YCP.24 16 PLIP interactions: 13 interactions with chain I, 3 interactions with chain H Hydrogen bonds: I:A.30, I:A.30, I:Q.32, I:L.33, I:S.56, I:N.78, I:V.92, I:A.119, H:N.252 Water bridges: I:G.31, I:A.34, I:K.93, I:K.93, I:T.146, H:N.252, H:S.255 NAI.29: 27 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, L.61, 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: YCP.15 15 PLIP interactions: 3 interactions with chain E, 12 interactions with chain J Hydrogen bonds: E:N.252, J:A.30, J:A.30, J:Q.32, J:L.33, J:S.56, J:N.78, J:V.92, J:A.119 Water bridges: E:N.252, E:S.255, J:G.31, J:A.34, J:T.146 Hydrophobic interactions: J:L.33

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

SO4.2: 3 residues within 4Å: Chain A: S.242, E.243, Q.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.243, A:Q.244 SO4.5: 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 SO4.8: 3 residues within 4Å: Chain C: S.242, E.243, Q.244 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.243, C:Q.244, C:Q.244 SO4.11: 3 residues within 4Å: Chain D: S.242, E.243, Q.244 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.241, D:E.243, D:Q.244 SO4.12: 3 residues within 4Å: Chain A: L.61, A.62 Chain D: R.222 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Salt bridges: D:R.222 Hydrogen bonds: A:A.62 SO4.17: 3 residues within 4Å: Chain F: S.242, E.243, Q.244 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.243, F:Q.244 SO4.20: 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 SO4.23: 3 residues within 4Å: Chain H: S.242, E.243, Q.244 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:E.243, H:Q.244, H:Q.244 SO4.26: 3 residues within 4Å: Chain I: S.242, E.243, Q.244 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:H.241, I:E.243, I:Q.244 SO4.27: 3 residues within 4Å: Chain F: L.61, A.62 Chain I: R.222 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain F Salt bridges: I:R.222 Hydrogen bonds: F:A.62

10 x YCP: (2S)-piperidine-2-carboxylic acid(Non-covalent)

YCP.3: 11 residues within 4Å: Chain A: V.253, S.254, S.255, G.258, A.259, T.260 Chain B: A.119, T.193, G.197, S.198 Ligands: NAI.4 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.255, A:A.259, A:T.260, A:T.260, A:T.260, A:T.260 Water bridges: A:S.255, A:G.258 Hydrophobic interactions: B:A.119, B:T.193 YCP.6: 10 residues within 4Å: Chain A: A.119, T.193, G.197 Chain B: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: NAI.1 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.255, B:A.259, B:T.260, B:T.260, B:T.260 Water bridges: B:S.255, B:S.255, B:G.258 Hydrophobic interactions: A:A.119, A:T.193 YCP.9: 11 residues within 4Å: Chain C: V.253, S.254, S.255, G.258, A.259, T.260 Chain D: A.119, T.193, G.197, S.198 Ligands: NAI.10 10 PLIP interactions: 8 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, C:T.260 Water bridges: C:S.255, C:G.258 Hydrophobic interactions: D:A.119, D:T.193 YCP.13: 11 residues within 4Å: Chain C: A.119, T.193, G.197, S.198 Chain D: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: NAI.7 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.255, D:A.259, D:T.260, D:T.260, D:T.260 Water bridges: D:S.255, D:S.255, D:G.258 Hydrophobic interactions: C:A.119, C:T.193 YCP.15: 11 residues within 4Å: Chain E: V.253, S.254, S.255, G.258, A.259, T.260 Chain J: A.119, T.193, G.197, S.198 Ligands: NAI.29 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain J Hydrogen bonds: E:S.255, E:A.259, E:T.260, E:T.260, E:T.260, E:T.260 Water bridges: E:S.255, E:G.258 Hydrophobic interactions: J:A.119, J:T.193 YCP.18: 11 residues within 4Å: Chain F: V.253, S.254, S.255, G.258, A.259, T.260 Chain G: A.119, T.193, G.197, S.198 Ligands: NAI.19 10 PLIP interactions: 2 interactions with chain G, 8 interactions with chain F Hydrophobic interactions: G:A.119, G:T.193 Hydrogen bonds: F:S.255, F:A.259, F:T.260, F:T.260, F:T.260, F:T.260 Water bridges: F:S.255, F:G.258 YCP.21: 10 residues within 4Å: Chain F: A.119, T.193, G.197 Chain G: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: NAI.16 10 PLIP interactions: 8 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:S.255, G:A.259, G:T.260, G:T.260, G:T.260 Water bridges: G:S.255, G:S.255, G:G.258 Hydrophobic interactions: F:A.119, F:T.193 YCP.24: 11 residues within 4Å: Chain H: V.253, S.254, S.255, G.258, A.259, T.260 Chain I: A.119, T.193, G.197, S.198 Ligands: NAI.25 10 PLIP interactions: 8 interactions with chain H, 2 interactions with chain I Hydrogen bonds: H:S.255, H:A.259, H:T.260, H:T.260, H:T.260, H:T.260 Water bridges: H:S.255, H:G.258 Hydrophobic interactions: I:A.119, I:T.193 YCP.28: 11 residues within 4Å: Chain H: A.119, T.193, G.197, S.198 Chain I: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: NAI.22 10 PLIP interactions: 2 interactions with chain H, 8 interactions with chain I Hydrophobic interactions: H:A.119, H:T.193 Hydrogen bonds: I:S.255, I:A.259, I:T.260, I:T.260, I:T.260 Water bridges: I:S.255, I:S.255, I:G.258 YCP.30: 11 residues within 4Å: Chain E: A.119, T.193, G.197, S.198 Chain J: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: NAI.14 10 PLIP interactions: 8 interactions with chain J, 2 interactions with chain E Hydrogen bonds: J:S.255, J:A.259, J:T.260, J:T.260, J:T.260, J:T.260 Water bridges: J:S.255, J:G.258 Hydrophobic interactions: E:A.119, E:T.193

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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