SMTL ID : 4gyp.1

Crystal structure of the heterotetrameric complex of GlucD and GlucDRP from E. coli K-12 MG1655 (EFI TARGET EFI-506058)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.235, N.237, E.260, D.261, N.289 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.235, A:D.235, A:E.260, A:D.261 MG.5: 5 residues within 4Å: Chain B: D.235, N.237, E.260, D.261, N.289 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.235, B:D.235, B:E.260, B:D.261

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 9 residues within 4Å: Chain A: N.27, H.32, T.103, Y.150, F.152, K.207, N.341, H.368, R.422 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.103, A:N.341 Water bridges: A:K.207, A:K.207, A:K.207, A:R.422 Salt bridges: A:H.32, A:K.207, A:H.368, A:R.422 SO4.6: 9 residues within 4Å: Chain B: N.27, H.32, T.103, Y.150, F.152, K.207, N.341, H.368, R.422 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:T.103, B:N.341 Water bridges: B:T.103, B:K.207, B:D.235, B:N.342, B:R.422 Salt bridges: B:H.32, B:K.207, B:H.368, B:R.422

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: G.299, L.302, S.303 Chain B: L.302, Q.305, F.332 Chain D: R.291 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:G.299, A:S.303, D:R.291 Water bridges: A:H.300, B:Q.305 GOL.8: 6 residues within 4Å: Chain A: L.302, F.332 Chain B: G.299, L.302, S.303 Chain C: R.291 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.302, A:F.332, B:G.299, B:S.303 Water bridges: A:Q.305 GOL.12: 8 residues within 4Å: Chain D: V.95, Q.96, H.99, W.306, T.329, S.331, G.332, R.335 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:W.306, D:T.329, D:R.335, D:R.335 Water bridges: D:Q.96 GOL.13: 5 residues within 4Å: Chain D: R.388, D.414, E.416, Q.417, K.420 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.388, D:D.414, D:E.416 Water bridges: D:K.420

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 7 residues within 4Å: Chain A: H.49, Q.126, H.127, L.128, G.129, P.396 Chain B: F.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.47, A:S.47 PEG.9: 8 residues within 4Å: Chain C: L.91, N.92, L.132, L.135, L.146 Chain D: N.92, L.135, L.146 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.92, D:N.92 Water bridges: D:N.92, C:N.92, C:N.92 PEG.14: 3 residues within 4Å: Chain D: T.346, N.372, P.373 No protein-ligand interaction detected (PLIP)

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.7: 10 residues within 4Å: Chain C: N.38, I.39, H.43, F.163, K.218, N.248, H.350, N.352, H.379, R.433 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.248, C:N.352, C:R.433, C:R.433 Salt bridges: C:H.43, C:K.218, C:K.218, C:H.350, C:H.379, C:R.433 CIT.10: 12 residues within 4Å: Chain D: N.38, I.39, H.43, W.115, F.117, F.163, K.218, N.248, H.350, N.352, H.379, R.433 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:N.38, D:G.40, D:N.248, D:N.352, D:N.352, D:R.433, D:R.433 Water bridges: D:N.300, D:H.350 Salt bridges: D:H.43, D:K.218, D:K.218, D:K.218, D:H.350, D:H.379, D:R.433

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.11: 15 residues within 4Å: Chain B: K.253, R.279, R.280, T.282, G.283, L.284, P.285, D.308 Chain D: R.290, R.291, A.292, T.293, G.294, P.296, D.319 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.253 Water bridges: B:R.231, B:A.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lukk, T. et al., Glucarate dehydratase and its related protein from Escherichia coli form a heterotetrameric complex. to be published

Release Date

2012-09-12

Peptides

Glucarate dehydratase: AB
Glucarate dehydratase-related protein: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glucarate dehydratase

Glucarate dehydratase-related protein

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