SMTL ID : 1mv8.2 (1 other biounit)

1.55 A crystal structure of a ternary complex of GDP-mannose dehydrogenase from Psuedomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

GLC-FRU.1: 4 residues within 4Å: Chain B: L.194, D.195, A.196, P.197 4 PLIP interactions: 4 interactions with chain B Water bridges: B:D.195, B:D.195, B:D.195, B:D.195

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

NAD.2: 21 residues within 4Å: Chain A: G.7, G.9, Y.10, V.11, V.29, D.30, V.31, K.35, C.83, V.84, G.85, T.86, Y.98, V.102, E.105, S.123, T.124, E.157 Chain B: C.268, K.271, R.331 27 PLIP interactions: 17 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:Y.10, A:V.11, A:V.31, A:K.35, A:V.84, A:T.86, A:E.105, A:T.124, A:E.157, B:K.271, B:K.271 Water bridges: A:G.9, A:G.12, A:K.35, A:K.35, A:K.35, A:G.85, A:T.124, B:S.267, B:R.331, B:R.331, B:R.331, B:R.331, B:R.331 Salt bridges: A:K.35, B:R.331, B:R.331 NAD.6: 22 residues within 4Å: Chain A: K.271, R.331 Chain B: F.6, G.7, 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: 17 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:Y.10, B:V.11, B:V.31, B:K.35, B:V.84, B:G.85, B:T.86, B:T.86, B:E.105, B:T.124, B:T.124, A:K.271 Water bridges: B:G.9, B:G.12, B:K.35, 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 ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 3 residues within 4Å: Chain A: R.259 Ligands: ACY.4, GDX.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.259 ACY.4: 6 residues within 4Å: Chain A: R.259, P.260, G.261, V.420 Ligands: ACY.3, GDX.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.420 Hydrogen bonds: A:P.260 Water bridges: A:F.262 Salt bridges: A:R.259

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 1 residues within 4Å: Chain A: A.389 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.414

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

GDX.7: 24 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, A.263, F.264, G.265, C.268, L.269, F.323, K.324 23 PLIP interactions: 14 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:Y.256, B:Y.257, B:Y.257, B:Y.257, B:R.259, B:R.259, B:F.262, B:G.265, A:E.157, A:L.159, A:E.161, A:K.210, A:N.214, A:H.217, A:N.225 Water bridges: B:F.262, B:A.263, B:F.323, B:K.324, A:E.161 Salt bridges: B:K.324, B:K.324, A:K.210 GDX.8: 26 residues within 4Å: Chain A: L.251, Y.256, Y.257, M.258, R.259, G.261, F.262, A.263, 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 Ligands: ACY.3, ACY.4 21 PLIP interactions: 14 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:G.265, B:E.157, B:L.159, B:E.161, B:K.210, B:N.214, B:N.225 Water bridges: A:F.262, A:A.263, A:F.323, A:K.324 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., The crystal structure of GDP-mannose dehydrogenase: A key enzyme in alginate biosynthesis of 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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