SMTL ID : 3d3f.1 (2 other biounits)

Crystal Structure of Yvgn and cofactor NADPH from Bacillus subtilis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 29 residues within 4Å: Chain A: G.22, V.23, F.24, D.48, Y.53, K.78, H.111, W.112, S.140, N.141, Q.162, W.188, S.189, P.190, L.191, M.192, Q.193, G.194, L.197, A.214, I.229, P.230, K.231, S.232, I.233, K.234, R.237, E.240, N.241 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:F.24, A:W.188, A:W.188 Hydrogen bonds: A:V.23, A:F.24, A:D.48, A:Y.53, A:S.140, A:N.141, A:Q.162, A:S.189, A:L.191, A:Q.193, A:K.231, A:I.233, A:R.237, A:E.240, A:N.241 Salt bridges: A:K.231, A:K.234, A:R.237 pi-Stacking: A:W.188 pi-Cation interactions: A:R.237 NDP.2: 28 residues within 4Å: Chain B: G.22, V.23, F.24, D.48, Y.53, K.78, H.111, W.112, S.140, N.141, Q.162, W.188, S.189, P.190, L.191, M.192, Q.193, L.197, A.214, I.229, P.230, K.231, S.232, I.233, K.234, R.237, E.240, N.241 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:F.24, B:W.188, B:W.188 Hydrogen bonds: B:V.23, B:F.24, B:D.48, B:D.48, B:S.140, B:N.141, B:Q.162, B:S.189, B:S.189, B:L.191, B:Q.193, B:Q.193, B:K.231, B:S.232, B:I.233, B:R.237, B:E.240, B:N.241 Salt bridges: B:K.231, B:K.234, B:R.237 pi-Stacking: B:W.188 pi-Cation interactions: B:R.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lei, J. et al., Structural and biochemical analyses of YvgN and YtbE from Bacillus subtilis. Protein Sci. (2009)

Release Date

2009-04-28

Peptides

YvgN protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

YvgN protein

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