SMTL ID : 2e6h.1 (1 other biounit)

Crystal structure of E37A mutant of the stationary phase survival protein SurE from Thermus thermophilus HB8 cocrystallized with manganese and AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: D.8, D.9, N.96 Ligands: SO4.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.8, A:D.9 MN.7: 4 residues within 4Å: Chain B: D.8, D.9, N.96 Ligands: SO4.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.8, B:D.9 MN.14: 4 residues within 4Å: Chain C: D.8, D.9, N.96 Ligands: SO4.16 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.8, C:D.9 MN.17: 4 residues within 4Å: Chain D: D.8, D.9, N.96 Ligands: SO4.20 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.8, D:D.9

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

SO4.2: 7 residues within 4Å: Chain A: G.102, H.103, S.178, V.179, R.180, Y.182, R.214 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.103, A:S.178, A:R.180 Salt bridges: A:H.103, A:R.180, A:R.214 SO4.3: 1 residues within 4Å: Chain A: R.180 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.180 SO4.4: 8 residues within 4Å: Chain A: D.8, N.96, N.100, H.107, S.108, G.109, T.110 Ligands: MN.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.96, A:N.100, A:S.108, A:G.109, A:T.110, A:T.110 SO4.8: 8 residues within 4Å: Chain B: L.101, G.102, H.103, S.178, V.179, R.180, Y.182, R.214 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.103, B:S.178, B:R.180 Salt bridges: B:H.103, B:R.180, B:R.214 SO4.9: 3 residues within 4Å: Chain B: R.180, P.204, R.214 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.180, B:E.207 Salt bridges: B:R.180 SO4.10: 8 residues within 4Å: Chain B: D.8, N.96, N.100, H.107, S.108, G.109, T.110 Ligands: MN.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.8, B:N.96, B:N.100, B:S.108, B:G.109, B:T.110, B:T.110, B:T.110, B:T.110 SO4.15: 7 residues within 4Å: Chain C: G.102, H.103, S.178, V.179, R.180, Y.182, R.214 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.103, C:S.178, C:R.180, C:Y.182 Salt bridges: C:R.180, C:R.214 SO4.16: 7 residues within 4Å: Chain C: D.8, N.96, N.100, S.108, G.109, T.110 Ligands: MN.14 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.8, C:N.96, C:N.100, C:S.108, C:G.109, C:T.110 SO4.18: 7 residues within 4Å: Chain D: G.102, H.103, S.178, V.179, R.180, Y.182, R.214 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:H.103, D:S.178, D:R.180, D:Y.182 Salt bridges: D:H.103, D:R.180, D:R.214 SO4.19: 2 residues within 4Å: Chain D: R.180, P.204 2 PLIP interactions: 2 interactions with chain D Water bridges: D:R.180 Salt bridges: D:R.180 SO4.20: 7 residues within 4Å: Chain D: D.8, N.96, N.100, S.108, G.109, T.110 Ligands: MN.17 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.8, D:N.100, D:S.108, D:G.109, D:T.110, D:T.110

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: S.24, G.27, E.28, V.29, F.30, H.64, F.65, P.66 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.27, A:V.29, A:H.64 GOL.6: 6 residues within 4Å: Chain A: A.44, I.45, Q.116, L.119 Chain B: H.103, Y.182 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.45, A:Q.116 Water bridges: A:Q.116, B:H.107 GOL.11: 7 residues within 4Å: Chain B: S.24, G.27, E.28, V.29, H.64, F.65, P.66 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.27, B:V.29 GOL.12: 2 residues within 4Å: Chain B: Y.12 Chain D: Y.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.12 GOL.13: 5 residues within 4Å: Chain A: H.103, Y.182, P.202 Chain B: Q.116, L.119 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.116, B:Q.116 Water bridges: B:I.45 GOL.21: 5 residues within 4Å: Chain D: W.17, H.56, P.59, H.61, A.62 No protein-ligand interaction detected (PLIP)

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

5'-nucleotidase surE

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