SMTL ID : 6xam.1

Crystal structure of NzeB in complex with cyclo-(L-Trp-L-homoalanine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 21 residues within 4Å: Chain A: I.90, L.155, L.237, A.240, G.241, T.244, S.245, F.248, L.286, V.291, R.293, L.316, G.343, F.344, G.345, H.349, C.351, P.352, A.357 Ligands: WMA.2, WMA.3 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:I.90, A:L.155, A:L.237, A:A.240, A:F.248, A:L.286, A:V.291, A:L.316, A:F.344, A:F.344, A:P.352, A:A.357 Water bridges: A:S.64, A:Q.68, A:R.293, A:R.293, A:R.348, A:H.349 Salt bridges: A:R.293, A:H.349 pi-Stacking: A:F.344 Metal complexes: A:C.351, H2O.3

2 x WMA: (3S,6S)-3-ethyl-6-[(1H-indol-3-yl)methyl]piperazine-2,5-dione(Non-covalent)

WMA.2: 13 residues within 4Å: Chain A: Q.75, F.177, T.244, L.286, S.287, S.290, V.291, K.292, L.316, F.390, F.391 Ligands: HEM.1, WMA.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Q.75, A:F.177, A:T.244, A:L.286, A:V.291, A:F.390, A:F.391 Hydrogen bonds: A:S.287, A:S.287 Water bridges: A:S.287, A:K.292, A:K.292, A:E.317, A:E.317 WMA.3: 10 residues within 4Å: Chain A: Q.68, L.80, I.90, L.236, V.239, A.240, K.292, F.391 Ligands: HEM.1, WMA.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.80, A:L.236, A:V.239, A:A.240, A:F.391, A:F.391 Water bridges: A:S.64, A:S.64, A:Q.68, A:Q.68, A:Q.68, A:K.292, A:K.292, A:H.349

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

EDO.4: 2 residues within 4Å: Chain A: G.134, T.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.135, A:T.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shende, V.V. et al., Structure and Function of NzeB, a Versatile C-C and C-N Bond-Forming Diketopiperazine Dimerase. J.Am.Chem.Soc. (2020)

Release Date

2021-06-09

Peptides

NzeB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NzeB

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