SMTL ID : 3i6b.2 (2 other biounits)

Crystal structure of YrbI lacking the last 8 residues, in complex with Kdo and inorganic phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.32, D.34, D.125 Ligands: PO4.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.34, A:D.125, H2O.2 MG.3: 4 residues within 4Å: Chain B: D.32, D.34, D.125 Ligands: PO4.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.32, B:D.34, B:D.125 MG.6: 4 residues within 4Å: Chain C: D.32, D.34, D.125 Ligands: PO4.7 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.34, C:D.125 MG.8: 6 residues within 4Å: Chain D: D.32, D.34, D.125, I.128, D.129 Ligands: PO4.9 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.125 MG.11: 4 residues within 4Å: Chain E: D.32, D.34, D.125 Ligands: PO4.12 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.34, E:D.125, H2O.9 MG.13: 4 residues within 4Å: Chain F: D.32, D.34, D.125 Ligands: PO4.14 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.32, F:D.34, F:D.125 MG.16: 4 residues within 4Å: Chain G: D.32, D.34, D.125 Ligands: PO4.17 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.34, G:D.125 MG.18: 6 residues within 4Å: Chain H: D.32, D.34, D.125, I.128, D.129 Ligands: PO4.19 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.125

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 9 residues within 4Å: Chain A: D.32, V.33, D.34, T.76, G.77, R.78, K.102 Ligands: MG.1, KDO.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:V.33, A:D.34, A:D.34, A:I.75, A:I.75, A:T.76, A:G.77, A:R.78 Water bridges: A:K.102 Salt bridges: A:K.102 PO4.4: 9 residues within 4Å: Chain B: D.32, V.33, D.34, I.75, T.76, G.77, K.102, I.128 Ligands: MG.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.33, B:D.34, B:I.75, B:G.77 Salt bridges: B:K.102 PO4.7: 9 residues within 4Å: Chain C: D.32, V.33, D.34, I.75, T.76, G.77, K.102 Ligands: MG.6, KDO.10 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.32, C:V.33, C:D.34, C:D.34, C:T.76, C:G.77 Salt bridges: C:K.102 PO4.9: 10 residues within 4Å: Chain D: D.32, V.33, D.34, I.75, T.76, G.77, K.102, I.128, D.129 Ligands: MG.8 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.32, D:V.33, D:D.34, D:D.34, D:G.77 Salt bridges: D:K.102 PO4.12: 9 residues within 4Å: Chain E: D.32, V.33, D.34, T.76, G.77, R.78, K.102 Ligands: MG.11, KDO.15 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:V.33, E:D.34, E:D.34, E:D.34, E:I.75, E:I.75, E:G.77, E:R.78 Water bridges: E:K.102 Salt bridges: E:K.102 PO4.14: 9 residues within 4Å: Chain F: D.32, V.33, D.34, I.75, T.76, G.77, K.102, I.128 Ligands: MG.13 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:V.33, F:D.34, F:D.34, F:I.75, F:T.76, F:G.77 Salt bridges: F:K.102 PO4.17: 9 residues within 4Å: Chain G: D.32, V.33, D.34, I.75, T.76, G.77, K.102 Ligands: MG.16, KDO.20 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:D.32, G:V.33, G:D.34, G:T.76, G:T.76, G:G.77 Salt bridges: G:K.102 PO4.19: 10 residues within 4Å: Chain H: D.32, V.33, D.34, I.75, T.76, G.77, K.102, I.128, D.129 Ligands: MG.18 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:V.33, H:D.34, H:T.76, H:G.77 Salt bridges: H:K.102

4 x KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid(Non-covalent)(Post Translational Modification)

KDO.5: 12 residues within 4Å: Chain A: D.34, R.78 Chain B: N.55, V.56, D.58, G.59, Y.60, R.63, R.86, T.89, L.90 Ligands: PO4.2 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.90 Hydrogen bonds: B:G.59, B:G.59, B:R.63, B:R.86, A:R.78 Water bridges: B:Y.60, B:Y.60, B:R.86 Salt bridges: B:R.86 KDO.10: 13 residues within 4Å: Chain C: D.34, G.77, R.78 Chain D: N.55, V.56, D.58, G.59, Y.60, R.63, R.86, T.89, L.90 Ligands: PO4.7 12 PLIP interactions: 4 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:D.34, C:G.77, C:R.78, C:R.78, D:G.59, D:G.59, D:Y.60, D:R.63, D:R.86 Hydrophobic interactions: D:L.90 Water bridges: D:N.55 Salt bridges: D:R.86 KDO.15: 12 residues within 4Å: Chain E: D.34, R.78 Chain F: N.55, V.56, D.58, G.59, Y.60, R.63, R.86, T.89, L.90 Ligands: PO4.12 11 PLIP interactions: 9 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:L.90 Hydrogen bonds: F:G.59, F:G.59, F:R.63, F:R.86, E:D.34, E:R.78 Water bridges: F:Y.60, F:Y.60, F:R.86 Salt bridges: F:R.86 KDO.20: 13 residues within 4Å: Chain G: D.34, G.77, R.78 Chain H: N.55, V.56, D.58, G.59, Y.60, R.63, R.86, T.89, L.90 Ligands: PO4.17 11 PLIP interactions: 8 interactions with chain H, 3 interactions with chain G Hydrophobic interactions: H:L.90 Hydrogen bonds: H:G.59, H:G.59, H:Y.60, H:R.63, H:R.86, G:G.77, G:R.78, G:R.78 Water bridges: H:N.55 Salt bridges: H:R.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biswas, T. et al., The Tail of KdsC: CONFORMATIONAL CHANGES CONTROL THE ACTIVITY OF A HALOACID DEHALOGENASE SUPERFAMILY PHOSPHATASE. J.Biol.Chem. (2009)

Release Date

2009-09-01

Peptides

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase

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