SMTL ID : 2e6b.2 (2 other biounits)

Crystal structure of the stationary phase survival protein SurE from Thermus thermophilus HB8 in complex with magnesium and tungstate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.8, D.9, N.96 Ligands: WO4.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.8, A:D.9 MG.8: 4 residues within 4Å: Chain B: D.8, D.9, N.96 Ligands: WO4.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.8, B:D.9 MG.14: 4 residues within 4Å: Chain C: D.8, D.9, N.96 Ligands: WO4.15 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.8, C:D.9 MG.17: 4 residues within 4Å: Chain D: D.8, D.9, N.96 Ligands: WO4.18 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.8, D:D.9 MG.21: 4 residues within 4Å: Chain E: D.8, D.9, N.96 Ligands: WO4.22 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.8, E:D.9 MG.28: 4 residues within 4Å: Chain F: D.8, D.9, N.96 Ligands: WO4.29 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.8, F:D.9 MG.34: 4 residues within 4Å: Chain G: D.8, D.9, N.96 Ligands: WO4.35 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.8, G:D.9 MG.37: 4 residues within 4Å: Chain H: D.8, D.9, N.96 Ligands: WO4.38 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.8, H:D.9

8 x WO4: TUNGSTATE(VI)ION(Non-covalent)

WO4.2: 8 residues within 4Å: Chain A: D.8, D.9, N.96, N.100, S.108, G.109, T.110 Ligands: MG.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.96, A:N.100, A:S.108, A:G.109, A:T.110, A:T.110 Metal complexes: A:D.8 WO4.9: 8 residues within 4Å: Chain B: D.8, D.9, N.96, N.100, S.108, G.109, T.110 Ligands: MG.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.96, B:N.100, B:S.108, B:G.109, B:T.110 Metal complexes: B:D.8 WO4.15: 8 residues within 4Å: Chain C: D.8, D.9, N.96, N.100, S.108, G.109, T.110 Ligands: MG.14 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.96, C:N.100, C:S.108, C:G.109, C:T.110, C:T.110 Metal complexes: C:D.8 WO4.18: 8 residues within 4Å: Chain D: D.8, D.9, N.96, N.100, S.108, G.109, T.110 Ligands: MG.17 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.96, D:N.100, D:S.108, D:G.109, D:T.110, D:T.110 Metal complexes: D:D.8 WO4.22: 8 residues within 4Å: Chain E: D.8, D.9, N.96, N.100, S.108, G.109, T.110 Ligands: MG.21 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:N.96, E:N.100, E:S.108, E:G.109, E:T.110 Metal complexes: E:D.8 WO4.29: 8 residues within 4Å: Chain F: D.8, D.9, N.96, N.100, S.108, G.109, T.110 Ligands: MG.28 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:N.96, F:N.100, F:S.108, F:G.109, F:T.110, F:T.110 Metal complexes: F:D.8 WO4.35: 8 residues within 4Å: Chain G: D.8, D.9, N.96, N.100, S.108, G.109, T.110 Ligands: MG.34 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:N.96, G:N.100, G:S.108, G:G.109, G:T.110 Metal complexes: G:D.8 WO4.38: 8 residues within 4Å: Chain H: D.8, D.9, N.96, N.100, S.108, G.109, T.110 Ligands: MG.37 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:N.96, H:N.100, H:S.108, H:G.109, H:T.110 Metal complexes: H:D.8

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

SO4.3: 7 residues within 4Å: Chain A: G.102, H.103, S.178, V.179, R.180, Y.182, R.214 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.180, P.204, R.214 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: R.228, L.229, D.230 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: T.235, R.236, P.239, T.240 Ligand excluded by PLIP SO4.10: 8 residues within 4Å: Chain B: L.101, G.102, H.103, S.178, V.179, R.180, Y.182, R.214 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain B: R.180, P.204, R.214 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain A: I.45, Q.116 Chain B: H.103, Y.182, P.202 Ligand excluded by PLIP SO4.16: 8 residues within 4Å: Chain C: L.101, G.102, H.103, S.178, V.179, R.180, Y.182, R.214 Ligand excluded by PLIP SO4.19: 7 residues within 4Å: Chain D: G.102, H.103, S.178, V.179, R.180, Y.182, R.214 Ligand excluded by PLIP SO4.20: 1 residues within 4Å: Chain D: R.180 Ligand excluded by PLIP SO4.23: 7 residues within 4Å: Chain E: G.102, H.103, S.178, V.179, R.180, Y.182, R.214 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain E: R.180, P.204, R.214 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain E: R.228, L.229, D.230 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain E: T.235, R.236, P.239, T.240 Ligand excluded by PLIP SO4.30: 8 residues within 4Å: Chain F: L.101, G.102, H.103, S.178, V.179, R.180, Y.182, R.214 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain F: R.180, P.204, R.214 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain E: I.45, Q.116 Chain F: H.103, Y.182, P.202 Ligand excluded by PLIP SO4.36: 8 residues within 4Å: Chain G: L.101, G.102, H.103, S.178, V.179, R.180, Y.182, R.214 Ligand excluded by PLIP SO4.39: 7 residues within 4Å: Chain H: G.102, H.103, S.178, V.179, R.180, Y.182, R.214 Ligand excluded by PLIP SO4.40: 1 residues within 4Å: Chain H: R.180 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: S.24, G.27, E.28, V.29, H.64, F.65, P.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.24 GOL.13: 6 residues within 4Å: Chain B: E.28, V.29, F.30, H.64, F.65, P.66 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.29, B:V.29 GOL.27: 7 residues within 4Å: Chain E: S.24, G.27, E.28, V.29, H.64, F.65, P.66 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.24 GOL.33: 6 residues within 4Å: Chain F: E.28, V.29, F.30, H.64, F.65, P.66 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:V.29, F:V.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iwasaki, W. et al., Crystal Structure of the Stationary Phase Survival Protein SurE with Metal Ion and AMP. J.Mol.Biol. (2007)

Release Date

2007-08-28

Peptides

5'-nucleotidase surE: 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

5'-nucleotidase surE

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