SMTL ID : 6pbm.1

Pseudopaline Dehydrogenase with NADP+ bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 23 residues within 4Å: Chain A: G.31, L.32, G.33, A.34, V.35, N.55, H.56, R.60, C.111, V.112, P.113, A.114, S.116, V.120, S.139, Y.166, A.168, A.169, T.170, T.231, R.376, E.380 Ligands: EDO.2 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:Y.166 Hydrogen bonds: A:L.32, A:L.32, A:A.34, A:V.35, A:N.55, A:A.114, A:T.170, A:T.170, A:E.380 Water bridges: A:G.33, A:A.36, A:R.60, A:R.60, A:R.60, A:R.60, A:R.60, A:R.60, A:R.60, A:S.139, A:S.139, A:T.170, A:R.376, A:R.376, A:R.376 Salt bridges: A:H.56, A:R.60, A:R.60, A:R.376, A:R.376 pi-Stacking: A:H.56 NAP.5: 27 residues within 4Å: Chain B: V.30, G.31, L.32, G.33, A.34, V.35, L.54, N.55, H.56, G.58, R.60, C.111, V.112, P.113, A.114, S.116, D.119, V.120, S.139, Y.166, A.168, A.169, T.170, K.171, K.187, R.376, E.380 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:Y.166 Hydrogen bonds: B:L.32, B:L.32, B:A.34, B:V.35, B:N.55, B:H.56, B:R.60, B:T.170, B:T.170, B:E.380, B:E.380 Water bridges: B:G.33, B:A.36, B:H.56, B:P.57, B:R.60, B:R.60, B:R.60, B:S.116, B:S.116, B:D.119, B:K.171, B:R.376 Salt bridges: B:H.56 pi-Stacking: B:H.56, B:H.56

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

EDO.2: 8 residues within 4Å: Chain A: V.30, G.31, L.54, N.55, H.56, V.112, V.120 Ligands: NAP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.55, A:H.56 EDO.3: 9 residues within 4Å: Chain A: Y.191, R.228, P.293, L.294, N.295, R.298, F.299, D.302, D.303 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.295, A:R.298, A:R.298 Water bridges: A:Y.191, A:P.293, A:D.303 EDO.4: 7 residues within 4Å: Chain A: G.241, A.274, R.277, Q.401, S.404, L.405, S.408 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.277, A:Q.401, A:S.404 EDO.6: 8 residues within 4Å: Chain A: K.260, V.341, R.352, D.355 Chain B: K.260, V.341, R.352, D.355 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.355, B:D.355 Water bridges: A:K.260, A:R.352, A:D.355, B:K.260, B:R.352 EDO.7: 7 residues within 4Å: Chain B: G.241, E.242, F.243, P.266, I.267, T.268, A.271 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.242, B:F.243, B:P.266 Water bridges: B:A.244 EDO.8: 6 residues within 4Å: Chain B: W.279, C.280, S.283, R.287, P.293, A.321 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.287, B:R.287 EDO.9: 6 residues within 4Å: Chain B: A.114, D.115, F.141, R.383, K.384, L.387 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.384, B:L.387 EDO.10: 7 residues within 4Å: Chain B: P.346, A.347, D.348, R.352, H.353, F.354, D.355 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.346 EDO.11: 6 residues within 4Å: Chain B: Y.259, N.304, R.335, Y.336, L.339, F.356 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.335, B:R.335 Water bridges: B:N.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McFarlane, J.S. et al., Staphylopine and pseudopaline dehydrogenase from bacterial pathogens catalyze reversible reactions and produce stereospecific metallophores. J.Biol.Chem. (2019)

Release Date

2019-10-30

Peptides

Pseudopaline Dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pseudopaline Dehydrogenase

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