SMTL ID : 5njc.1 (1 other biounit)

E. coli Microcin-processing metalloprotease TldD/E (TldD E263A mutant) with hexapeptide bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

hetero-1-1-mer

Ligands

1 x VAL- LEU- GLU- ASP- ARG- ILE: VAL-LEU-GLU-ASP-ARG-ILE(Non-covalent)

VAL-LEU-GLU-ASP-ARG-ILE.1: 19 residues within 4Å: Chain A: R.198, W.270, V.273, H.276, H.281, F.287, F.405, G.407, G.408, Q.409, V.410, I.412, V.465, G.466, V.467, C.468, G.469, K.470 Ligands: ZN.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:W.270, A:V.273, A:H.281, A:F.287, A:I.412, A:V.465, A:K.470 Hydrogen bonds: A:G.408, A:G.408, A:V.410, A:V.467, A:V.467, A:G.469, A:G.469, A:E.471 Water bridges: A:Q.409, A:V.410 Salt bridges: A:R.198, A:H.276, A:H.281

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.276, H.281, C.468 Ligands: VAL-LEU-GLU-ASP-ARG-ILE.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.276, A:H.281, A:C.468

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

MES.3: 9 residues within 4Å: Chain A: R.45, R.46, L.47, D.48, G.118, D.119, K.121, V.122, T.185 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.47, A:D.119, A:T.185 Water bridges: A:R.46, A:G.120 Salt bridges: A:D.119 MES.6: 6 residues within 4Å: Chain B: D.34, Y.71, H.72, Q.73, N.74, A.109 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.34, B:N.74, B:N.74 Water bridges: B:Q.73 Salt bridges: B:D.34

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: D.48, Y.49, I.85, K.350, L.351, R.354 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.354 EDO.7: 3 residues within 4Å: Chain A: E.88 Chain B: R.51, Y.52 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.88, B:R.51 Water bridges: A:E.88 EDO.8: 4 residues within 4Å: Chain B: M.213, S.214, L.216, T.218 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.214, B:L.216 Water bridges: B:T.218 EDO.9: 3 residues within 4Å: Chain B: M.242, K.243, K.446 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.243, B:K.446 EDO.10: 4 residues within 4Å: Chain B: W.288, Q.356, V.423, T.424 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.424, B:T.424

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 1 residues within 4Å: Chain A: S.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.131, A:S.131 NA.11: 2 residues within 4Å: Chain B: S.30, S.33 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghilarov, D. et al., The Origins of Specificity in the Microcin-Processing Protease TldD/E. Structure (2017)

Release Date

2017-10-04

Peptides

Metalloprotease TldD: A
Metalloprotease PmbA: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Metalloprotease TldD

Metalloprotease PmbA

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