SMTL ID : 5uau.1 (3 other biounits)

Structure of human PYCR-1 complexed with proline

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-10-mer

Ligands

20 x PRO: PROLINE(Non-covalent)

PRO.1: 8 residues within 4Å: Chain A: V.253, S.255, G.258, A.259, T.260 Chain B: A.119, T.193, G.197 10 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: B:A.119, B:T.193 Hydrogen bonds: A:V.253, A:S.255, A:A.259, A:T.260, A:T.260, A:T.260, P.1, P.1 PRO.2: 5 residues within 4Å: Chain A: A.158, T.159, V.184, E.185, E.186 5 PLIP interactions: 5 interactions with chain A, Hydrogen bonds: A:T.159, A:E.185, A:E.186 Water bridges: A:E.183, A:E.186 PRO.3: 8 residues within 4Å: Chain A: T.193, G.197, S.198 Chain B: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: P.3, B:V.253, B:S.255, B:A.259, B:T.260, B:T.260 Hydrophobic interactions: A:T.193 PRO.4: 3 residues within 4Å: Chain B: T.159, E.185, E.186 4 PLIP interactions: 4 interactions with chain B, Hydrogen bonds: B:T.159, B:E.186 Water bridges: B:E.185, B:D.187 PRO.6: 9 residues within 4Å: Chain C: V.253, S.255, G.258, A.259, T.260 Chain D: A.119, T.193, G.197, S.198 10 PLIP interactions: 6 interactions with chain C, 2 Ligand-Ligand interactions, 2 interactions with chain D Hydrogen bonds: C:V.253, C:S.255, C:A.259, C:T.260, C:T.260, C:T.260, P.6, P.6 Hydrophobic interactions: D:A.119, D:T.193 PRO.7: 5 residues within 4Å: Chain C: A.158, T.159, V.184, E.185, E.186 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:T.159, C:T.159, C:V.184, C:E.186, P.7 Water bridges: C:D.187 PRO.9: 7 residues within 4Å: Chain C: T.193, G.197 Chain D: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 1 interactions with chain C, 5 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: C:T.193 Hydrogen bonds: D:S.255, D:A.259, D:T.260, D:T.260, D:T.260, P.9 PRO.10: 3 residues within 4Å: Chain D: T.159, E.185, E.186 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:T.159, D:E.186, P.10, P.10 Water bridges: D:E.185, D:D.187 PRO.12: 8 residues within 4Å: Chain E: V.253, S.255, G.258, A.259, T.260 Chain J: A.119, T.193, G.197 10 PLIP interactions: 2 interactions with chain J, 2 Ligand-Ligand interactions, 6 interactions with chain E Hydrophobic interactions: J:A.119, J:T.193 Hydrogen bonds: P.12, P.12, E:V.253, E:S.255, E:A.259, E:T.260, E:T.260, E:T.260 PRO.13: 5 residues within 4Å: Chain E: A.158, T.159, V.184, E.185, E.186 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain E Hydrogen bonds: P.13, E:T.159, E:T.159, E:V.184, E:E.186 PRO.15: 8 residues within 4Å: Chain F: V.253, S.255, G.258, A.259, T.260 Chain G: A.119, T.193, G.197 10 PLIP interactions: 6 interactions with chain F, 2 Ligand-Ligand interactions, 2 interactions with chain G Hydrogen bonds: F:V.253, F:S.255, F:A.259, F:T.260, F:T.260, F:T.260, P.15, P.15 Hydrophobic interactions: G:A.119, G:T.193 PRO.16: 5 residues within 4Å: Chain F: A.158, T.159, V.184, E.185, E.186 5 PLIP interactions: 5 interactions with chain F, Hydrogen bonds: F:T.159, F:E.185, F:E.186 Water bridges: F:E.183, F:E.186 PRO.17: 8 residues within 4Å: Chain F: T.193, G.197, S.198 Chain G: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 1 interactions with chain F, 5 interactions with chain G, 1 Ligand-Ligand interactions Hydrophobic interactions: F:T.193 Hydrogen bonds: G:V.253, G:S.255, G:A.259, G:T.260, G:T.260, P.17 PRO.18: 3 residues within 4Å: Chain G: T.159, E.185, E.186 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:T.159, G:E.186 Water bridges: G:E.185, G:D.187 PRO.20: 9 residues within 4Å: Chain H: V.253, S.255, G.258, A.259, T.260 Chain I: A.119, T.193, G.197, S.198 10 PLIP interactions: 2 interactions with chain I, 6 interactions with chain H, 2 Ligand-Ligand interactions Hydrophobic interactions: I:A.119, I:T.193 Hydrogen bonds: H:V.253, H:S.255, H:A.259, H:T.260, H:T.260, H:T.260, P.20, P.20 PRO.21: 5 residues within 4Å: Chain H: A.158, T.159, V.184, E.185, E.186 6 PLIP interactions: 5 interactions with chain H, 1 Ligand-Ligand interactions Hydrogen bonds: H:T.159, H:T.159, H:V.184, H:E.186, P.21 Water bridges: H:D.187 PRO.23: 7 residues within 4Å: Chain H: T.193, G.197 Chain I: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain I, 1 interactions with chain H Hydrogen bonds: P.23, I:S.255, I:A.259, I:T.260, I:T.260, I:T.260 Hydrophobic interactions: H:T.193 PRO.24: 3 residues within 4Å: Chain I: T.159, E.185, E.186 6 PLIP interactions: 4 interactions with chain I, 2 Ligand-Ligand interactions Hydrogen bonds: I:T.159, I:E.186, P.24, P.24 Water bridges: I:E.185, I:D.187 PRO.26: 8 residues within 4Å: Chain E: A.119, T.193, G.197 Chain J: V.253, S.255, G.258, A.259, T.260 10 PLIP interactions: 6 interactions with chain J, 2 Ligand-Ligand interactions, 2 interactions with chain E Hydrogen bonds: J:V.253, J:S.255, J:A.259, J:T.260, J:T.260, J:T.260, P.26, P.26 Hydrophobic interactions: E:A.119, E:T.193 PRO.27: 5 residues within 4Å: Chain J: A.158, T.159, V.184, E.185, E.186 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Ligand interactions Hydrogen bonds: J:T.159, J:T.159, J:V.184, J:E.186, P.27

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

SO4.5: 4 residues within 4Å: Chain B: G.31, Q.32, L.33, A.91 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.32, B:L.33 SO4.8: 3 residues within 4Å: Chain C: G.31, Q.32, L.33 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.31, C:Q.32, C:L.33 SO4.11: 4 residues within 4Å: Chain D: G.31, Q.32, L.33, A.91 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.32, D:L.33, D:A.91 SO4.14: 4 residues within 4Å: Chain E: G.31, Q.32, L.33, A.91 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.32, E:L.33 SO4.19: 4 residues within 4Å: Chain G: G.31, Q.32, L.33, A.91 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.32, G:L.33 SO4.22: 3 residues within 4Å: Chain H: G.31, Q.32, L.33 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:G.31, H:Q.32, H:L.33 SO4.25: 4 residues within 4Å: Chain I: G.31, Q.32, L.33, A.91 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:Q.32, I:L.33, I:A.91 SO4.28: 4 residues within 4Å: Chain J: G.31, Q.32, L.33, A.91 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:Q.32, J:L.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Christensen, E.M. et al., Resolving the cofactor-binding site in the proline biosynthetic enzyme human pyrroline-5-carboxylate reductase 1. J. Biol. Chem. (2017)

Release Date

2017-03-15

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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