SMTL ID : 2izz.1

Crystal structure of human pyrroline-5-carboxylate reductase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-10-mer

Ligands

10 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.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, T.146 Chain B: N.252, V.253, S.255 Ligands: EDO.3 16 PLIP interactions: 13 interactions with chain A, 3 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, B:S.255 Water bridges: A:G.31, A:Q.32, A:A.34, B:S.255 Salt bridges: A:K.93, A:K.93 NAD.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, T.146 Ligands: EDO.2, EDO.4 13 PLIP interactions: 1 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: B:G.31, B:A.34 Salt bridges: B:K.93, B:K.93 NAD.6: 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, T.146 Chain D: N.252, V.253 Ligands: EDO.8, EDO.10 15 PLIP interactions: 14 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:Q.32, C:A.34, C:K.93 Salt bridges: C:K.93, C:K.93 NAD.9: 27 residues within 4Å: Chain C: N.252, V.253, S.255 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, T.146 Ligands: EDO.7 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.33 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 NAD.11: 25 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: V.253 Ligands: EDO.12 14 PLIP interactions: 13 interactions with chain E, 1 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 Water bridges: E:G.31, E:A.34, E:T.146, J:T.260 Salt bridges: E:K.93, E:K.93 NAD.13: 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, T.146 Chain G: N.252, V.253, S.255 Ligands: EDO.15 16 PLIP interactions: 3 interactions with chain G, 13 interactions with chain F Hydrogen bonds: G:N.252, G:S.255, F:A.30, F:A.30, F:Q.32, F:L.33, F:S.56, F:N.78, F:V.92, F:A.119 Water bridges: G:S.255, F:G.31, F:Q.32, F:A.34 Salt bridges: F:K.93, F:K.93 NAD.17: 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, T.146 Ligands: EDO.14, EDO.16 13 PLIP interactions: 12 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 Salt bridges: G:K.93, G:K.93 NAD.18: 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, T.146 Chain I: N.252, V.253 Ligands: EDO.20, EDO.22 15 PLIP interactions: 1 interactions with chain I, 14 interactions with chain H Hydrogen bonds: I:N.252, H:A.30, H:A.30, H:Q.32, H:L.33, H:S.56, H:N.78, H:V.92, H:A.119 Water bridges: H:G.31, H:Q.32, H:A.34, H:K.93 Salt bridges: H:K.93, H:K.93 NAD.21: 27 residues within 4Å: Chain H: N.252, V.253, S.255 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, T.146 Ligands: EDO.19 12 PLIP interactions: 11 interactions with chain I, 1 interactions with chain H Hydrophobic interactions: I:L.33 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 NAD.23: 25 residues within 4Å: Chain E: 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: EDO.24 13 PLIP interactions: 13 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 Salt bridges: J:K.93, J:K.93

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: V.253, T.260 Chain B: A.119, T.193, G.197 Ligands: NAD.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.253, A:T.260 Water bridges: A:A.259 EDO.3: 6 residues within 4Å: Chain A: A.119, T.193, G.197 Chain B: V.253, T.260 Ligands: NAD.1 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.253, B:T.260 Water bridges: B:S.255, B:A.259 EDO.4: 6 residues within 4Å: Chain A: D.251, N.252, S.255, P.256 Chain B: K.93 Ligands: NAD.5 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.252, B:K.93 EDO.7: 7 residues within 4Å: Chain C: V.253, S.255, T.260 Chain D: A.119, T.193, G.197 Ligands: NAD.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.253, C:T.260, C:T.260 Water bridges: C:A.259, C:A.259 EDO.8: 6 residues within 4Å: Chain C: A.119, T.193, G.197 Chain D: V.253, T.260 Ligands: NAD.6 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:V.253, D:T.260 Water bridges: D:S.255, D:A.259 EDO.10: 7 residues within 4Å: Chain C: Q.32, K.93 Chain D: D.251, N.252, S.255, P.256 Ligands: NAD.6 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:K.93 Water bridges: C:Q.32, D:S.254 EDO.12: 6 residues within 4Å: Chain E: K.93 Chain J: N.252, S.254, S.255, P.256 Ligands: NAD.11 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.93 EDO.14: 6 residues within 4Å: Chain F: V.253, T.260 Chain G: A.119, T.193, G.197 Ligands: NAD.17 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:V.253, F:T.260 Water bridges: F:A.259 EDO.15: 6 residues within 4Å: Chain F: A.119, T.193, G.197 Chain G: V.253, T.260 Ligands: NAD.13 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:V.253, G:T.260 Water bridges: G:S.255, G:A.259 EDO.16: 6 residues within 4Å: Chain F: D.251, N.252, S.255, P.256 Chain G: K.93 Ligands: NAD.17 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:N.252, G:K.93 EDO.19: 7 residues within 4Å: Chain H: V.253, S.255, T.260 Chain I: A.119, T.193, G.197 Ligands: NAD.21 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:V.253, H:T.260 Water bridges: H:A.259, H:A.259 EDO.20: 6 residues within 4Å: Chain H: A.119, T.193, G.197 Chain I: V.253, T.260 Ligands: NAD.18 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:V.253, I:T.260 Water bridges: I:S.255, I:A.259 EDO.22: 7 residues within 4Å: Chain H: Q.32, K.93 Chain I: D.251, N.252, S.255, P.256 Ligands: NAD.18 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:K.93 Water bridges: H:Q.32, I:S.254 EDO.24: 6 residues within 4Å: Chain E: N.252, S.254, S.255, P.256 Chain J: K.93 Ligands: NAD.23 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:K.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pike, A.C.W. et al., Crystal Structure of Human Pyrroline-5-Carboxylate Reductase. To be Published

Release Date

2006-08-01

Peptides

PYRROLINE-5-CARBOXYLATE REDUCTASE 1: 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

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