SMTL ID : 4ejm.1

Crystal structure of a putative zinc-binding dehydrogenase (Target PSI-012003) from Sinorhizobium meliloti 1021 bound to NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.111, G.112, C.114, C.117, C.125 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.117, A:C.125 ZN.6: 5 residues within 4Å: Chain B: C.111, G.112, C.114, C.117, C.125 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.111, B:C.114, B:C.117, B:C.125 ZN.11: 5 residues within 4Å: Chain C: C.111, G.112, C.114, C.117, C.125 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.111, C:C.114, C:C.117, C:C.125 ZN.16: 5 residues within 4Å: Chain D: C.111, G.112, C.114, C.117, C.125 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.111, D:C.114, D:C.117, D:C.125

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

NAP.2: 25 residues within 4Å: Chain A: C.170, G.190, G.191, G.192, V.193, I.194, S.213, T.214, R.215, Q.216, K.219, P.234, C.260, A.261, G.262, V.263, E.265, T.266, L.283, G.284, V.285, S.309, F.310, I.311 Chain C: L.300 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:I.194 Hydrogen bonds: A:G.191, A:G.192, A:I.194, A:T.214, A:T.214, A:R.215, A:Q.216, A:K.219, A:A.261, A:E.265, A:L.283, A:V.285, A:I.311 Water bridges: A:G.61, A:G.61, A:V.193, A:V.193, A:G.195, A:Q.269, A:V.285 Salt bridges: A:R.215, A:K.219 pi-Cation interactions: A:R.215 NAP.7: 25 residues within 4Å: Chain B: C.170, G.190, G.191, G.192, V.193, I.194, S.213, T.214, R.215, Q.216, K.219, P.234, C.260, A.261, G.262, V.263, E.265, T.266, L.283, G.284, V.285, S.309, F.310, I.311 Chain D: L.300 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.194 Hydrogen bonds: B:G.191, B:G.192, B:I.194, B:T.214, B:T.214, B:R.215, B:Q.216, B:K.219, B:A.261, B:E.265, B:L.283, B:V.285, B:I.311 Water bridges: B:G.61, B:G.61, B:V.193, B:V.193, B:G.195, B:Q.269, B:V.285 Salt bridges: B:R.215, B:K.219 pi-Cation interactions: B:R.215 NAP.12: 25 residues within 4Å: Chain A: L.300 Chain C: C.170, G.190, G.191, G.192, V.193, I.194, S.213, T.214, R.215, Q.216, K.219, P.234, C.260, A.261, G.262, V.263, E.265, T.266, L.283, G.284, V.285, S.309, F.310, I.311 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:I.194 Hydrogen bonds: C:G.191, C:G.192, C:I.194, C:T.214, C:R.215, C:Q.216, C:K.219, C:A.261, C:E.265, C:L.283, C:V.285, C:I.311 Water bridges: C:G.61, C:G.61, C:V.193, C:V.193, C:G.195, C:Q.269, C:V.285 Salt bridges: C:R.215, C:K.219 pi-Cation interactions: C:R.215 NAP.17: 25 residues within 4Å: Chain B: L.300 Chain D: C.170, G.190, G.191, G.192, V.193, I.194, S.213, T.214, R.215, Q.216, K.219, P.234, C.260, A.261, G.262, V.263, E.265, T.266, L.283, G.284, V.285, S.309, F.310, I.311 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:I.194 Hydrogen bonds: D:G.191, D:G.192, D:I.194, D:T.214, D:R.215, D:Q.216, D:K.219, D:A.261, D:E.265, D:L.283, D:V.285, D:I.311 Water bridges: D:G.61, D:G.61, D:V.193, D:V.193, D:G.195, D:Q.269, D:V.285 Salt bridges: D:R.215, D:K.219 pi-Cation interactions: D:R.215

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

EDO.3: 3 residues within 4Å: Chain A: R.220, R.221, E.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.220, A:E.224 Water bridges: A:T.231 EDO.4: 5 residues within 4Å: Chain A: H.173, D.176, P.313, F.314, V.315 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.176 EDO.5: 4 residues within 4Å: Chain A: Q.116, L.124 Chain C: A.276, F.301 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.301 EDO.8: 3 residues within 4Å: Chain B: R.220, R.221, E.224 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.220, B:E.224 Water bridges: B:T.231 EDO.9: 5 residues within 4Å: Chain B: H.173, D.176, P.313, F.314, V.315 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.176 EDO.10: 4 residues within 4Å: Chain B: Q.116, L.124 Chain D: A.276, F.301 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.301 EDO.13: 3 residues within 4Å: Chain C: R.220, R.221, E.224 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.220, C:E.224 EDO.14: 5 residues within 4Å: Chain C: H.173, D.176, P.313, F.314, V.315 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.173, C:D.176, C:D.176 EDO.15: 4 residues within 4Å: Chain A: A.276, F.301 Chain C: Q.116, L.124 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.301 EDO.18: 3 residues within 4Å: Chain D: R.220, R.221, E.224 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.220, D:E.224 EDO.19: 5 residues within 4Å: Chain D: H.173, D.176, P.313, F.314, V.315 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.173, D:D.176, D:D.176 EDO.20: 4 residues within 4Å: Chain B: A.276, F.301 Chain D: Q.116, L.124 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.301

Links

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Citation

Sampathkumar, P. et al., Crystal structure of a putative zinc-binding dehydrogenase (target nysgrc-012003) from sinorhizobium meliloti 1021 bound to NADP. To be Published

Release Date

2012-05-02

Peptides

Putative zinc-binding dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Putative zinc-binding dehydrogenase

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