SMTL ID : 1muu.2 (1 other biounit)

2.0 A crystal structure of GDP-mannose dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 8 residues within 4Å: Chain A: K.315, A.389, S.390, S.391, D.392, S.412, G.413, K.414 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.315, A:S.412, A:S.412 Hydrogen bonds: A:K.315, A:K.315, A:D.392, A:G.413, A:K.414

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

NAD.2: 24 residues within 4Å: Chain A: F.6, G.7, L.8, G.9, Y.10, V.11, V.29, D.30, V.31, K.35, C.83, V.84, G.85, T.86, Y.98, T.101, V.102, E.105, S.123, T.124, E.157 Chain B: S.267, K.271, R.331 24 PLIP interactions: 8 interactions with chain B, 16 interactions with chain A Hydrogen bonds: B:S.267, B:K.271, B:K.271, A:L.8, A:Y.10, A:V.11, A:V.31, A:K.35, A:V.84, A:G.85, A:T.86, A:E.105, A:T.124, A:E.157 Water bridges: B:R.331, B:R.331, B:R.331, A:G.9, A:G.12, A:T.101, A:T.124 Salt bridges: B:R.331, B:R.331, A:K.35 NAD.3: 23 residues within 4Å: Chain A: K.271, R.331 Chain B: F.6, G.7, L.8, G.9, Y.10, V.11, V.29, D.30, V.31, K.35, C.83, V.84, G.85, T.86, Y.98, T.101, V.102, E.105, S.123, T.124, E.157 25 PLIP interactions: 16 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:L.8, B:Y.10, B:V.11, B:V.31, B:K.35, B:V.84, B:G.85, B:T.86, B:E.105, B:T.124, B:T.124, A:K.271, A:K.271 Water bridges: B:G.9, B:G.12, B:K.35, B:K.35, A:S.267, A:R.331, A:R.331, A:R.331, A:R.331 Salt bridges: B:K.35, A:R.331, A:R.331

2 x GDX: GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER(Non-covalent)

GDX.4: 23 residues within 4Å: Chain A: E.157, F.158, L.159, R.160, E.161, K.210, N.214, H.217, V.221, N.225 Chain B: L.251, Y.256, Y.257, M.258, R.259, G.261, F.262, F.264, G.265, C.268, L.269, F.323, K.324 23 PLIP interactions: 9 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:E.157, A:L.159, A:E.161, A:K.210, A:N.214, A:H.217, A:N.225, B:Y.256, B:Y.257, B:Y.257, B:R.259, B:R.259, B:F.262, B:F.262, B:G.265, B:F.323 Water bridges: A:E.161, B:C.268, B:K.324, B:D.329 Salt bridges: A:K.210, B:K.324, B:K.324 GDX.5: 23 residues within 4Å: Chain A: L.251, Y.256, Y.257, M.258, R.259, G.261, F.262, F.264, G.265, C.268, L.269, F.323, K.324 Chain B: E.157, F.158, L.159, R.160, E.161, K.210, N.214, H.217, V.221, N.225 19 PLIP interactions: 12 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:Y.256, A:Y.256, A:Y.257, A:Y.257, A:R.259, A:R.259, A:F.262, A:F.262, A:G.265, A:F.323, B:E.157, B:L.159, B:E.161, B:K.210, B:N.214, B:N.225 Salt bridges: A:K.324, A:K.324, B:K.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Snook, C.F. et al., Crystal structure of GDP-mannose dehydrogenase: A key enzyme of alginate biosynthesis in P. aeruginosa. Biochemistry (2003)

Release Date

2003-05-06

Peptides

GDP-mannose 6-dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

GDP-mannose 6-dehydrogenase

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