SMTL ID : 7kf3.1

Crystal structure of GDP-mannose 4,6-dehydratase from Brucella abortus (strain 2308) in complex with Guanosine-diphosphate-rhamnose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x GDR: GUANOSINE-5'-DIPHOSPHATE-RHAMNOSE(Non-covalent)

GDR.1: 25 residues within 4Å: Chain A: S.90, H.91, V.92, T.133, S.134, E.135, Y.157, N.186, R.192, T.195, F.196, V.197, K.200, Y.217, L.218, G.219, N.220, S.223, R.225, V.259, Y.301, R.303, E.306, V.307 Ligands: NAP.2 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:E.135 Hydrogen bonds: A:S.90, A:V.92, A:Y.157, A:Y.157, A:R.192, A:R.192, A:T.195, A:T.195, A:V.197, A:K.200, A:G.219, A:N.220, A:S.223, A:R.303, A:V.307 Water bridges: A:S.90, A:N.186, A:N.186, A:R.225, A:Y.301, A:R.303, A:R.303, A:E.306 Salt bridges: A:R.192, A:R.303, A:R.303 GDR.3: 24 residues within 4Å: Chain B: S.90, H.91, V.92, T.133, S.134, E.135, Y.157, N.186, R.192, T.195, F.196, V.197, K.200, L.218, G.219, N.220, S.223, R.225, V.259, Y.301, R.303, E.306, V.307 Ligands: NAP.4 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:E.135 Hydrogen bonds: B:S.90, B:V.92, B:T.133, B:Y.157, B:R.192, B:R.192, B:T.195, B:T.195, B:V.197, B:K.200, B:G.219, B:N.220, B:S.223, B:R.303, B:V.307 Water bridges: B:S.90, B:N.186, B:N.186, B:N.186, B:R.225, B:R.303, B:R.303, B:E.306 Salt bridges: B:R.192, B:R.303, B:R.303 GDR.5: 23 residues within 4Å: Chain C: S.90, V.92, T.133, S.134, E.135, Y.157, N.186, R.192, T.195, F.196, V.197, K.200, L.218, G.219, N.220, S.223, R.225, V.259, Y.301, R.303, E.306, V.307 Ligands: NAP.6 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:E.135 Hydrogen bonds: C:S.90, C:V.92, C:T.133, C:Y.157, C:R.192, C:R.192, C:T.195, C:T.195, C:V.197, C:K.200, C:G.219, C:N.220, C:S.223, C:R.303, C:V.307 Water bridges: C:S.90, C:N.186, C:R.225, C:R.225, C:R.303, C:R.303, C:R.303, C:E.306 Salt bridges: C:R.192, C:R.303, C:R.303 GDR.7: 23 residues within 4Å: Chain D: S.90, V.92, T.133, S.134, E.135, Y.157, N.186, R.192, T.195, F.196, V.197, K.200, L.218, G.219, N.220, S.223, R.225, V.259, Y.301, R.303, E.306, V.307 Ligands: NAP.8 30 PLIP interactions: 30 interactions with chain D Hydrophobic interactions: D:E.135 Hydrogen bonds: D:S.90, D:V.92, D:Y.157, D:Y.157, D:R.192, D:R.192, D:T.195, D:T.195, D:V.197, D:K.200, D:G.219, D:N.220, D:S.223, D:R.303, D:V.307 Water bridges: D:S.90, D:N.186, D:N.186, D:N.186, D:T.198, D:R.225, D:Y.301, D:R.303, D:R.303, D:E.306, D:E.306 Salt bridges: D:R.192, D:R.303, D:R.303

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

NAP.2: 31 residues within 4Å: Chain A: G.9, T.11, G.12, Q.13, D.14, R.34, N.40, D.64, L.65, L.86, G.87, A.88, Q.89, S.90, Y.101, S.105, A.131, S.132, T.133, Y.157, K.161, L.184, F.185, N.186, H.187, E.188, R.192 Chain B: R.35, T.36, S.37 Ligands: GDR.1 35 PLIP interactions: 30 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.9, A:T.11, A:T.11, A:T.11, A:G.12, A:Q.13, A:Q.13, A:D.14, A:D.14, A:N.40, A:D.64, A:L.65, A:L.86, A:A.88, A:S.90, A:Y.101, A:K.161, A:H.187, A:H.187, A:R.192, B:R.35, B:S.37, B:S.37 Water bridges: A:I.10, A:G.15, A:R.34, A:R.34, A:R.34, A:S.90, A:S.90, A:G.193, B:T.36, B:Q.38 Salt bridges: A:R.34 pi-Cation interactions: A:R.34 NAP.4: 31 residues within 4Å: Chain A: R.35, T.36, S.37 Chain B: G.9, T.11, G.12, Q.13, D.14, R.34, N.40, D.64, L.65, L.86, G.87, A.88, Q.89, S.90, Y.101, S.105, A.131, S.132, T.133, Y.157, K.161, L.184, F.185, N.186, H.187, E.188, R.192 Ligands: GDR.3 34 PLIP interactions: 30 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.9, B:T.11, B:T.11, B:T.11, B:G.12, B:Q.13, B:Q.13, B:D.14, B:D.14, B:N.40, B:D.64, B:L.65, B:L.86, B:A.88, B:S.90, B:Y.101, B:Y.157, B:K.161, B:H.187, B:H.187, B:R.192, A:R.35, A:S.37, A:S.37 Water bridges: B:G.15, B:R.34, B:R.34, B:R.34, B:A.88, B:S.90, B:G.193, A:Q.38 Salt bridges: B:R.34 pi-Cation interactions: B:R.34 NAP.6: 32 residues within 4Å: Chain C: G.9, I.10, T.11, G.12, Q.13, D.14, R.34, N.40, D.64, L.65, L.86, G.87, A.88, Q.89, S.90, Y.101, S.105, A.131, S.132, T.133, Y.157, K.161, L.184, F.185, N.186, H.187, E.188, R.192 Chain D: R.35, T.36, S.37 Ligands: GDR.5 34 PLIP interactions: 30 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.9, C:T.11, C:G.12, C:Q.13, C:Q.13, C:D.14, C:N.40, C:D.64, C:L.65, C:L.86, C:A.88, C:S.90, C:Y.101, C:Y.157, C:K.161, C:H.187, C:H.187, C:R.192, D:R.35, D:S.37, D:S.37 Water bridges: C:I.10, C:T.11, C:T.11, C:T.11, C:G.15, C:R.34, C:R.34, C:R.34, C:S.90, C:G.193, D:Q.38 Salt bridges: C:R.34 pi-Cation interactions: C:R.34 NAP.8: 31 residues within 4Å: Chain C: R.35, T.36, S.37 Chain D: G.9, T.11, G.12, Q.13, D.14, R.34, N.40, D.64, L.65, L.86, G.87, A.88, Q.89, S.90, Y.101, S.105, A.131, S.132, T.133, Y.157, K.161, L.184, F.185, N.186, H.187, E.188, R.192 Ligands: GDR.7 34 PLIP interactions: 29 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:G.9, D:T.11, D:T.11, D:T.11, D:G.12, D:Q.13, D:Q.13, D:D.14, D:N.40, D:D.64, D:L.65, D:L.86, D:A.88, D:S.90, D:Y.101, D:K.161, D:H.187, D:H.187, D:R.192, D:R.192, C:R.35, C:S.37, C:S.37 Water bridges: D:G.9, D:G.9, D:G.15, D:R.34, D:A.88, D:S.90, D:G.193, C:S.37, C:Q.38 Salt bridges: D:R.34 pi-Cation interactions: D:R.34

Links

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Citation

Abendroth, J. et al., Crystal structure of GDP-mannose 4,6-dehydratase from Brucella abortus (strain 2308) in complex with Guanosine-diphosphate-rhamnose. to be published

Release Date

2020-11-04

Peptides

GDP-mannose 4,6-dehydratase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GDP-mannose 4,6-dehydratase