SMTL ID : 5udx.1

LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with zinc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: D.231 Chain B: D.231 Chain C: D.231 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:D.231, B:D.231, C:D.231, C:D.231, H2O.1 ZN.2: 2 residues within 4Å: Chain A: H.190 Ligands: SO4.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.190, H2O.1, H2O.1 ZN.9: 2 residues within 4Å: Chain B: D.218 Chain D: H.216 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Metal complexes: D:H.216, B:D.218 ZN.12: 3 residues within 4Å: Chain D: D.231 Chain E: D.231 Chain F: D.231 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: E:D.231, E:D.231, D:D.231, D:D.231, H2O.2 ZN.13: 2 residues within 4Å: Chain D: D.59, D.63 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.59, D:D.63, D:D.63 ZN.19: 3 residues within 4Å: Chain F: E.55, D.82, H.190 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.55, F:E.55, F:D.82, F:D.82, F:H.190

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

PO4.3: 6 residues within 4Å: Chain A: C.176, S.180, R.181, R.212, R.214, R.259 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.180, A:R.181 Salt bridges: A:R.212, A:R.214, A:R.259 PO4.7: 6 residues within 4Å: Chain B: C.176, S.180, R.212, R.214, F.258, R.259 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.180 Water bridges: B:R.259 Salt bridges: B:R.212, B:R.214, B:R.259 PO4.10: 5 residues within 4Å: Chain C: C.176, S.180, R.212, R.214, R.259 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.180, C:S.180, C:S.180 Salt bridges: C:R.212, C:R.214, C:R.259 PO4.14: 6 residues within 4Å: Chain D: C.176, S.180, R.212, R.214, F.258, R.259 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.180 Salt bridges: D:R.212, D:R.214, D:R.259 PO4.17: 5 residues within 4Å: Chain E: C.176, S.180, R.212, R.214, R.259 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:S.180, E:S.180, E:R.181 Salt bridges: E:R.212, E:R.214, E:R.259 PO4.20: 5 residues within 4Å: Chain F: C.176, S.180, R.212, R.214, R.259 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.180, F:S.180 Salt bridges: F:R.212, F:R.214, F:R.259

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

SO4.4: 6 residues within 4Å: Chain A: S.26, G.28, I.29, D.30, S.31, G.123 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.26, A:S.26, A:G.28, A:D.30, A:S.31, A:G.123 SO4.5: 4 residues within 4Å: Chain A: K.90, T.189, H.190 Ligands: ZN.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.190 Salt bridges: A:K.90, A:H.190 SO4.6: 5 residues within 4Å: Chain A: W.97, K.101, K.137, A.138, R.139 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.138, A:R.139 Salt bridges: A:K.101, A:R.139 SO4.8: 5 residues within 4Å: Chain B: S.26, G.28, I.29, D.30, S.31 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.26, B:G.28, B:D.30, B:D.30, B:S.31, B:S.31 SO4.11: 6 residues within 4Å: Chain C: S.26, G.28, I.29, D.30, S.31, G.123 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.26, C:G.28, C:D.30, C:S.31 SO4.15: 6 residues within 4Å: Chain D: S.26, G.28, I.29, D.30, S.31, G.123 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.26, D:G.28, D:D.30, D:S.31 SO4.16: 3 residues within 4Å: Chain D: D.86, H.88, Y.99 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.88 SO4.18: 4 residues within 4Å: Chain E: S.26, G.28, D.30, S.31 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:S.26, E:G.28, E:D.30, E:D.30, E:S.31 SO4.21: 5 residues within 4Å: Chain F: S.26, G.28, D.30, S.31, G.123 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.26, F:G.28, F:D.30, F:S.31, F:S.31 SO4.22: 4 residues within 4Å: Chain F: K.90, T.189, H.190, D.191 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:H.190, F:D.191, F:D.191 Salt bridges: F:K.90, F:H.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fellner, M. et al., Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-08-23

Peptides

Lactate racemization operon protein LarE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Lactate racemization operon protein LarE

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