SMTL ID : 1k1e.4 (4 other biounits)

Structure Of the cobalt-bound form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-octamer

Ligands

8 x CO: COBALT (II) ION(Non-covalent)

CO.1: 4 residues within 4Å: Chain A: D.14, D.16, D.107, D.111 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.14, A:D.16, A:D.107, H2O.1, H2O.1, H2O.1 CO.6: 4 residues within 4Å: Chain B: D.14, D.16, D.107, D.111 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.14, B:D.16, B:D.107, H2O.5, H2O.5, H2O.5 CO.11: 4 residues within 4Å: Chain C: D.14, D.16, D.107, D.111 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.14, C:D.16, C:D.107, H2O.8, H2O.8, H2O.8 CO.16: 4 residues within 4Å: Chain D: D.14, D.16, D.107, D.111 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.14, D:D.16, D:D.107, H2O.13, H2O.13, H2O.13 CO.19: 4 residues within 4Å: Chain E: D.14, D.16, D.107, D.111 6 PLIP interactions: 3 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.14, E:D.16, E:D.107, H2O.16, H2O.16, H2O.17 CO.24: 4 residues within 4Å: Chain F: D.14, D.16, D.107, D.111 6 PLIP interactions: 3 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.14, F:D.16, F:D.107, H2O.21, H2O.21, H2O.21 CO.29: 4 residues within 4Å: Chain G: D.14, D.16, D.107, D.111 6 PLIP interactions: 3 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.14, G:D.16, G:D.107, H2O.24, H2O.24, H2O.24 CO.34: 4 residues within 4Å: Chain H: D.14, D.16, D.107, D.111 6 PLIP interactions: 3 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.14, H:D.16, H:D.107, H2O.29, H2O.29, H2O.29

8 x HG: MERCURY (II) ION(Non-covalent)

HG.2: 4 residues within 4Å: Chain A: C.88, Y.104, A.114, C.118 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.88, A:C.118 HG.7: 5 residues within 4Å: Chain B: C.88, M.92, Y.104, A.114, C.118 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.88, B:A.114, B:C.118 HG.12: 5 residues within 4Å: Chain C: C.88, M.92, Y.104, A.114, C.118 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.88, C:A.114, C:C.118 HG.17: 4 residues within 4Å: Chain D: C.88, Y.104, A.114, C.118 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.88, D:C.118 HG.20: 4 residues within 4Å: Chain E: C.88, Y.104, A.114, C.118 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:C.88, E:C.118 HG.25: 5 residues within 4Å: Chain F: C.88, M.92, Y.104, A.114, C.118 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.88, F:A.114, F:C.118 HG.30: 5 residues within 4Å: Chain G: C.88, M.92, Y.104, A.114, C.118 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.88, G:A.114, G:C.118 HG.35: 4 residues within 4Å: Chain H: C.88, Y.104, A.114, C.118 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:C.88, H:C.118

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

SO4.3: 6 residues within 4Å: Chain A: D.14, S.58, G.59, L.82, K.84, V.110 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.14, A:G.59 Water bridges: A:D.16, A:D.16, A:D.16, A:D.16 Salt bridges: A:K.84 SO4.4: 3 residues within 4Å: Chain A: T.167, A.168, Q.169 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.168, A:Q.169 SO4.8: 6 residues within 4Å: Chain B: D.14, S.58, G.59, L.82, K.84, V.110 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.14, B:G.59 Water bridges: B:V.15, B:D.16, B:D.16, B:K.84 Salt bridges: B:K.84 SO4.9: 3 residues within 4Å: Chain B: T.167, A.168, Q.169 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.168, B:Q.169 SO4.13: 6 residues within 4Å: Chain C: D.14, S.58, G.59, R.60, K.84, V.110 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.14, C:G.59 Water bridges: C:V.15, C:D.16, C:D.16, C:D.16, C:R.60 Salt bridges: C:R.60, C:K.84 SO4.18: 5 residues within 4Å: Chain D: D.14, S.58, G.59, K.84, V.110 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.14, D:G.59 Water bridges: D:D.16, D:D.16, D:D.16 Salt bridges: D:K.84 SO4.21: 6 residues within 4Å: Chain E: D.14, S.58, G.59, L.82, K.84, V.110 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:D.14, E:G.59 Water bridges: E:V.15, E:D.16, E:D.16 Salt bridges: E:K.84 SO4.22: 3 residues within 4Å: Chain E: T.167, A.168, Q.169 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:A.168, E:Q.169 SO4.26: 6 residues within 4Å: Chain F: D.14, S.58, G.59, L.82, K.84, V.110 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:D.14, F:G.59 Water bridges: F:V.15, F:D.16, F:D.16, F:K.84 Salt bridges: F:K.84 SO4.27: 3 residues within 4Å: Chain F: T.167, A.168, Q.169 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:A.168, F:Q.169 SO4.31: 6 residues within 4Å: Chain G: D.14, S.58, G.59, R.60, K.84, V.110 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:D.14, G:G.59 Water bridges: G:V.15, G:D.16, G:D.16, G:R.60, G:R.60 Salt bridges: G:R.60, G:K.84 SO4.36: 5 residues within 4Å: Chain H: D.14, S.58, G.59, K.84, V.110 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:D.14, H:G.59 Water bridges: H:V.15, H:D.16, H:D.16 Salt bridges: H:K.84

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: D.90, K.93, Q.94 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.94 GOL.14: 3 residues within 4Å: Chain C: D.90, K.93, Q.94 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.94 GOL.15: 4 residues within 4Å: Chain C: K.75, L.76, F.77, Q.94 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.77, C:F.77, C:Q.94, C:Q.94 GOL.23: 3 residues within 4Å: Chain E: D.90, K.93, Q.94 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.94 GOL.32: 3 residues within 4Å: Chain G: D.90, K.93, Q.94 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.94 GOL.33: 4 residues within 4Å: Chain G: K.75, L.76, F.77, Q.94 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:F.77, G:F.77, G:Q.94, G:Q.94

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.10: 8 residues within 4Å: Chain A: Q.23, I.33 Chain B: Q.23, H.25, I.33 Chain C: Q.23, H.25 Chain D: Q.23 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: B:Q.23, A:Q.23, C:Q.23, D:Q.23 MES.28: 8 residues within 4Å: Chain E: Q.23, I.33 Chain F: Q.23, H.25, I.33 Chain G: Q.23, H.25 Chain H: Q.23 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain G, 1 interactions with chain E, 1 interactions with chain H Hydrogen bonds: F:Q.23, G:Q.23, E:Q.23, H:Q.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parsons, J.F. et al., From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase. Proteins (2002)

Release Date

2002-02-27

Peptides

deoxy-D-mannose-octulosonate 8-phosphate phosphatase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
L

E
I

F
J

G
K

H
L

deoxy-D-mannose-octulosonate 8-phosphate phosphatase

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