SMTL ID : 3hk8.1 (1 other biounit)

Crystal structure of uronate isomerase from Bacillus halodurans complexed with zinc and D-Arabinohydroxamate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x HDL: D-arabinohydroxamic acid(Non-covalent)

HDL.1: 12 residues within 4Å: Chain A: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.28, A:Y.50, A:D.355, A:R.357 Water bridges: A:S.223, A:W.326 Salt bridges: A:H.26, A:H.28, A:R.170 HDL.6: 11 residues within 4Å: Chain B: H.26, H.28, H.49, Y.50, R.170, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.28, B:D.355, B:R.357 Water bridges: B:Y.50, B:S.223 Salt bridges: B:H.26, B:H.28, B:R.170 HDL.11: 12 residues within 4Å: Chain C: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.13 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:H.28, C:Y.50, C:D.355, C:R.357 Water bridges: C:S.223, C:W.326 Salt bridges: C:H.26, C:H.28, C:R.170 HDL.16: 11 residues within 4Å: Chain D: H.26, H.28, H.49, Y.50, R.170, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.18 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:H.28, D:D.355, D:R.357 Water bridges: D:Y.50, D:S.223 Salt bridges: D:H.26, D:H.28, D:R.170 HDL.21: 12 residues within 4Å: Chain E: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.23 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:H.28, E:Y.50, E:D.355, E:R.357 Water bridges: E:S.223, E:W.326 Salt bridges: E:H.26, E:H.28, E:R.170 HDL.26: 11 residues within 4Å: Chain F: H.26, H.28, H.49, Y.50, R.170, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.28 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:H.28, F:D.355, F:R.357 Water bridges: F:Y.50, F:S.223 Salt bridges: F:H.26, F:H.28, F:R.170

6 x CO3: CARBONATE ION(Non-functional Binders)

CO3.2: 8 residues within 4Å: Chain A: H.49, Y.50, A.53, A.272, W.326, F.327 Chain C: R.314, K.315 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:H.49, C:R.314, C:K.315, C:K.315 CO3.7: 8 residues within 4Å: Chain B: H.49, Y.50, A.53, A.272, W.326, F.327 Chain F: R.314, K.315 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain F Hydrogen bonds: B:H.49, F:R.314, F:K.315, F:K.315 CO3.12: 8 residues within 4Å: Chain C: H.49, Y.50, A.53, A.272, W.326, F.327 Chain E: R.314, K.315 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:H.49, E:R.314, E:K.315, E:K.315 CO3.17: 8 residues within 4Å: Chain B: R.314, K.315 Chain D: H.49, Y.50, A.53, A.272, W.326, F.327 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.314, B:K.315, B:K.315, D:H.49 CO3.22: 8 residues within 4Å: Chain A: R.314, K.315 Chain E: H.49, Y.50, A.53, A.272, W.326, F.327 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:H.49, A:R.314, A:K.315, A:K.315 CO3.27: 8 residues within 4Å: Chain D: R.314, K.315 Chain F: H.49, Y.50, A.53, A.272, W.326, F.327 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:R.314, D:K.315, D:K.315, F:H.49

12 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.26, H.28, D.355 Ligands: HDL.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.26, A:H.28, A:D.355 ZN.4: 5 residues within 4Å: Chain A: E.332 Chain C: E.332 Chain E: E.332 Ligands: ZN.14, ZN.24 No protein-ligand interaction detected (PLIP) ZN.8: 4 residues within 4Å: Chain B: H.26, H.28, D.355 Ligands: HDL.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.26, B:H.28, B:D.355 ZN.9: 5 residues within 4Å: Chain B: E.332 Chain D: E.332 Chain F: E.332 Ligands: ZN.19, ZN.29 No protein-ligand interaction detected (PLIP) ZN.13: 4 residues within 4Å: Chain C: H.26, H.28, D.355 Ligands: HDL.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.26, C:H.28, C:D.355 ZN.14: 5 residues within 4Å: Chain A: E.332 Chain C: E.332 Chain E: E.332 Ligands: ZN.4, ZN.24 No protein-ligand interaction detected (PLIP) ZN.18: 4 residues within 4Å: Chain D: H.26, H.28, D.355 Ligands: HDL.16 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.26, D:H.28, D:D.355 ZN.19: 5 residues within 4Å: Chain B: E.332 Chain D: E.332 Chain F: E.332 Ligands: ZN.9, ZN.29 No protein-ligand interaction detected (PLIP) ZN.23: 4 residues within 4Å: Chain E: H.26, H.28, D.355 Ligands: HDL.21 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.26, E:H.28, E:D.355 ZN.24: 5 residues within 4Å: Chain A: E.332 Chain C: E.332 Chain E: E.332 Ligands: ZN.4, ZN.14 No protein-ligand interaction detected (PLIP) ZN.28: 4 residues within 4Å: Chain F: H.26, H.28, D.355 Ligands: HDL.26 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.26, F:H.28, F:D.355 ZN.29: 5 residues within 4Å: Chain B: E.332 Chain D: E.332 Chain F: E.332 Ligands: ZN.9, ZN.19 No protein-ligand interaction detected (PLIP)

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 8 residues within 4Å: Chain A: K.278, E.304 Chain C: K.278, E.304 Chain E: K.278, E.304 Ligands: CL.15, CL.25 Ligand excluded by PLIP CL.10: 8 residues within 4Å: Chain B: K.278, E.304 Chain D: K.278, E.304 Chain F: K.278, E.304 Ligands: CL.20, CL.30 Ligand excluded by PLIP CL.15: 8 residues within 4Å: Chain A: K.278, E.304 Chain C: K.278, E.304 Chain E: K.278, E.304 Ligands: CL.5, CL.25 Ligand excluded by PLIP CL.20: 8 residues within 4Å: Chain B: K.278, E.304 Chain D: K.278, E.304 Chain F: K.278, E.304 Ligands: CL.10, CL.30 Ligand excluded by PLIP CL.25: 8 residues within 4Å: Chain A: K.278, E.304 Chain C: K.278, E.304 Chain E: K.278, E.304 Ligands: CL.5, CL.15 Ligand excluded by PLIP CL.30: 8 residues within 4Å: Chain B: K.278, E.304 Chain D: K.278, E.304 Chain F: K.278, E.304 Ligands: CL.10, CL.20 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, T.T. et al., The mechanism of the reaction catalyzed by uronate isomerase illustrates how an isomerase may have evolved from a hydrolase within the amidohydrolase superfamily. Biochemistry (2009)

Release Date

2009-08-25

Peptides

Uronate isomerase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Uronate isomerase

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