SMTL ID : 8td3.1

Structure of PYCR1 complexed with NADH and (S)-Tetrahydro-2H-pyran-2-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-10-mer

Ligands

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

NAI.1: 26 residues within 4Å: Chain A: 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 B: N.252, V.253 Ligands: GJM.4 17 PLIP interactions: 15 interactions with chain A, 2 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:A.34, A:K.93, A:K.93, A:T.146, B:N.252 Salt bridges: A:K.93, A:K.93 NAI.5: 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: GJM.2 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.30, B:A.30, B:Q.32, B:L.33, B:S.56, B:N.78, B:V.92, B:A.119, A:N.252 Water bridges: B:G.31, B:A.34, B:T.146, A:N.252 Salt bridges: B:K.93, B:K.93 NAI.6: 27 residues within 4Å: Chain C: 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 D: N.252, V.253 Ligands: GJM.8 15 PLIP interactions: 13 interactions with chain C, 2 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:T.146, D:N.252 Salt bridges: C:K.93, C:K.93 NAI.9: 26 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, 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: GJM.7 17 PLIP interactions: 15 interactions with chain D, 2 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 Salt bridges: D:K.93, D:K.93 NAI.11: 26 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.100, C.117, A.118, A.119, M.143, T.144, N.145, T.146 Chain J: N.252, V.253 Ligands: GJM.26 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain J 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:K.93, E:T.146, J:N.252 Salt bridges: E:K.93, E:K.93 NAI.15: 26 residues within 4Å: Chain F: 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 G: N.252, V.253 Ligands: GJM.18 17 PLIP interactions: 15 interactions with chain F, 2 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:A.34, F:K.93, F:K.93, F:T.146, G:N.252 Salt bridges: F:K.93, F:K.93 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: GJM.16 15 PLIP interactions: 13 interactions with chain G, 2 interactions with chain F 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 Salt bridges: G:K.93, G:K.93 NAI.20: 27 residues within 4Å: Chain H: 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 I: N.252, V.253 Ligands: GJM.22 15 PLIP interactions: 13 interactions with chain H, 2 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:T.146, I:N.252 Salt bridges: H:K.93, H:K.93 NAI.23: 26 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, 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: GJM.21 17 PLIP interactions: 15 interactions with chain I, 2 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 Salt bridges: I:K.93, I:K.93 NAI.25: 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, L.61, N.78, A.91, V.92, K.93, P.94, I.100, C.117, A.118, A.119, M.143, T.144, N.145, T.146 Ligands: GJM.12 16 PLIP interactions: 14 interactions with chain J, 2 interactions with chain E Hydrogen bonds: J:A.30, J:A.30, J:Q.32, J:L.33, J:S.56, J:N.78, J:V.92, J:A.119, E:N.252 Water bridges: J:G.31, J:A.34, J:K.93, J:T.146, E:N.252 Salt bridges: J:K.93, J:K.93

10 x GJM: (2S)-oxane-2-carboxylic acid(Non-covalent)

GJM.2: 10 residues within 4Å: Chain A: V.253, S.254, S.255, A.259, T.260 Chain B: A.119, T.193, G.197, S.198 Ligands: NAI.5 12 PLIP interactions: 10 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 Water bridges: A:S.255, A:S.255, A:S.255, A:G.258, A:I.261 Hydrophobic interactions: B:A.119, B:T.193 GJM.4: 11 residues within 4Å: Chain A: A.119, T.193, G.197, S.198 Chain B: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: NAI.1 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.119, A:T.193 Hydrogen bonds: B:S.255, B:A.259, B:T.260 Water bridges: B:S.255, B:S.255, B:G.258 GJM.7: 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.9 9 PLIP interactions: 7 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 Water bridges: C:S.255, C:G.258 Hydrophobic interactions: D:A.119, D:T.193 GJM.8: 10 residues within 4Å: Chain C: A.119, T.193, G.197, S.198 Chain D: V.253, S.254, S.255, A.259, T.260 Ligands: NAI.6 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.255, D:A.259, D:T.260, D:T.260 Water bridges: D:S.255, D:S.255, D:S.255, D:S.255, D:G.258 Hydrophobic interactions: C:A.119, C:T.193 GJM.12: 9 residues within 4Å: Chain E: V.253, S.255, A.259, T.260 Chain J: A.119, T.193, G.197, S.198 Ligands: NAI.25 12 PLIP interactions: 10 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 Water bridges: E:S.255, E:S.255, E:S.255, E:G.258, E:I.261 Hydrophobic interactions: J:A.119, J:T.193 GJM.16: 10 residues within 4Å: Chain F: V.253, S.254, S.255, A.259, T.260 Chain G: A.119, T.193, G.197, S.198 Ligands: NAI.19 12 PLIP interactions: 2 interactions with chain G, 10 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 Water bridges: F:S.255, F:S.255, F:S.255, F:G.258, F:I.261 GJM.18: 11 residues within 4Å: Chain F: A.119, T.193, G.197, S.198 Chain G: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: NAI.15 9 PLIP interactions: 2 interactions with chain F, 7 interactions with chain G Hydrophobic interactions: F:A.119, F:T.193 Hydrogen bonds: G:S.255, G:A.259, G:T.260, G:T.260 Water bridges: G:S.255, G:S.255, G:G.258 GJM.21: 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.23 9 PLIP interactions: 7 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 Water bridges: H:S.255, H:G.258 Hydrophobic interactions: I:A.119, I:T.193 GJM.22: 10 residues within 4Å: Chain H: A.119, T.193, G.197, S.198 Chain I: V.253, S.254, S.255, A.259, T.260 Ligands: NAI.20 11 PLIP interactions: 2 interactions with chain H, 9 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 Water bridges: I:S.255, I:S.255, I:S.255, I:S.255, I:G.258 GJM.26: 9 residues within 4Å: Chain E: A.119, T.193, G.197, S.198 Chain J: V.253, S.255, A.259, T.260 Ligands: NAI.11 12 PLIP interactions: 2 interactions with chain E, 10 interactions with chain J Hydrophobic interactions: E:A.119, E:T.193 Hydrogen bonds: J:S.255, J:A.259, J:T.260, J:T.260, J:T.260 Water bridges: J:S.255, J:S.255, J:S.255, J:G.258, J:I.261

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

PEG.3: 7 residues within 4Å: Chain A: D.187, L.188, R.288 Chain B: M.217, G.218 Chain E: H.95 Chain J: P.256 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain A Water bridges: J:P.256 Hydrogen bonds: A:R.288 PEG.13: 6 residues within 4Å: Chain E: A.43, V.149, V.150, R.151 Chain J: K.237, H.241 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain E Hydrogen bonds: J:K.237, E:V.149 PEG.14: 4 residues within 4Å: Chain A: P.256 Chain E: G.218 Chain J: D.187, L.188 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain B Hydrogen bonds: J:D.187 Water bridges: J:R.288, B:H.95 PEG.17: 7 residues within 4Å: Chain E: P.256 Chain F: D.187, L.188, R.288 Chain G: M.217, G.218 Chain J: H.95 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Water bridges: F:R.288, E:P.256 PEG.27: 6 residues within 4Å: Chain E: K.237, H.241 Chain J: A.43, V.149, V.150, R.151 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain E Hydrogen bonds: J:V.149, E:K.237 PEG.28: 4 residues within 4Å: Chain E: D.187, L.188 Chain F: P.256 Chain J: G.218 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain G Hydrogen bonds: E:D.187 Water bridges: E:R.288, G:H.95

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.10: 7 residues within 4Å: Chain C: M.217, G.218 Chain D: D.187, L.188, R.288 Chain H: H.95 Chain I: P.256 No protein-ligand interaction detected (PLIP) PGE.24: 7 residues within 4Å: Chain C: H.95 Chain D: P.256 Chain H: M.217, G.218 Chain I: D.187, L.188, R.288 No protein-ligand interaction detected (PLIP)

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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