SMTL ID : 8dkg.1

Structure of PYCR1 Thr171Met variant complexed with NADH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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, 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, T.146 Chain B: N.252, V.253 Ligands: SO4.3 13 PLIP interactions: 12 interactions with chain A, 1 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:E.103, A:T.146 NAI.5: 23 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, N.78, A.91, V.92, K.93, P.94, I.96, I.100, C.117, A.118, A.119, T.144, T.146 12 PLIP interactions: 11 interactions with chain B, 1 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 NAI.7: 23 residues within 4Å: Chain C: 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, T.146 Chain D: V.253 Ligands: SO4.11 12 PLIP interactions: 11 interactions with chain C, 1 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 NAI.8: 23 residues within 4Å: Chain C: N.252, V.253 Chain D: 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, M.143, T.144, T.146 11 PLIP interactions: 10 interactions with chain D, 1 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, C:N.252 Water bridges: D:G.31, D:A.34, D:T.146 NAI.12: 20 residues within 4Å: Chain E: G.29, A.30, G.31, Q.32, L.33, S.56, P.57, N.78, A.91, V.92, K.93, P.94, I.96, I.100, C.117, A.118, A.119, T.144, T.146 Ligands: SO4.13 11 PLIP interactions: 11 interactions with chain E 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 Water bridges: E:G.31, E:A.34, E:T.146 NAI.14: 26 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, T.146 Chain G: N.252, V.253 Ligands: SO4.16 13 PLIP interactions: 12 interactions with chain F, 1 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:E.103, F:T.146 NAI.18: 23 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, N.78, A.91, V.92, K.93, P.94, I.96, I.100, C.117, A.118, A.119, T.144, T.146 12 PLIP interactions: 11 interactions with chain G, 1 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 NAI.20: 23 residues within 4Å: Chain H: 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, T.146 Chain I: V.253 Ligands: SO4.24 12 PLIP interactions: 11 interactions with chain H, 1 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 NAI.21: 23 residues within 4Å: Chain H: N.252, V.253 Chain I: 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, M.143, T.144, T.146 11 PLIP interactions: 10 interactions with chain I, 1 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, H:N.252 Water bridges: I:G.31, I:A.34, I:T.146 NAI.25: 20 residues within 4Å: Chain J: G.29, A.30, G.31, Q.32, L.33, S.56, P.57, N.78, A.91, V.92, K.93, P.94, I.96, I.100, C.117, A.118, A.119, T.144, T.146 Ligands: SO4.26 11 PLIP interactions: 11 interactions with chain J 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 Water bridges: J:G.31, J:A.34, J:T.146

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

SO4.2: 3 residues within 4Å: Chain A: S.242, E.243, Q.244 Ligand excluded by PLIP SO4.3: 1 residues within 4Å: Ligands: NAI.1 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: Q.32, L.61, A.62, T.63 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain B: S.242, E.243, Q.244 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain D: S.242, E.243, Q.244 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain D: Q.32, L.61, A.62, T.63 Ligand excluded by PLIP SO4.11: 8 residues within 4Å: Chain C: M.193 Chain D: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: NAI.7 Ligand excluded by PLIP SO4.13: 8 residues within 4Å: Chain E: M.193 Chain J: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: NAI.12 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain F: S.242, E.243, Q.244 Ligand excluded by PLIP SO4.16: 1 residues within 4Å: Ligands: NAI.14 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain F: Q.32, L.61, A.62, T.63 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain G: S.242, E.243, Q.244 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain I: S.242, E.243, Q.244 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain I: Q.32, L.61, A.62, T.63 Ligand excluded by PLIP SO4.24: 8 residues within 4Å: Chain H: M.193 Chain I: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: NAI.20 Ligand excluded by PLIP SO4.26: 8 residues within 4Å: Chain E: V.253, S.254, S.255, G.258, A.259, T.260 Chain J: M.193 Ligands: NAI.25 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Daudu, O.I. et al., Functional Impact of a Cancer-Related Variant in Human Delta 1 -Pyrroline-5-Carboxylate Reductase 1. Acs Omega (2023)

Release Date

2023-02-08

Peptides

Isoform 3 of 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

Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial