SMTL ID : 6xai.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

monomer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: I.90, L.150, L.155, L.236, A.240, G.241, T.244, S.245, F.248, L.281, L.286, V.291, R.293, L.316, G.343, F.344, G.345, H.349, C.351, P.352, L.356, A.357 Ligands: QRP.2, QRP.3 24 PLIP interactions: 23 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:I.90, A:L.150, A:L.155, A:L.155, A:L.236, A:A.240, A:F.248, A:L.281, A:L.286, A:V.291, A:L.316, A:F.344, A:F.344, A:L.356, A:A.357 Water bridges: A:Q.68, A:Q.68, A:R.293, A:R.293 Salt bridges: A:R.293, A:H.349 pi-Stacking: A:F.344 Metal complexes: A:C.351, H2O.6

2 x QRP: (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione(Non-covalent)

QRP.2: 14 residues within 4Å: Chain A: Q.75, E.76, T.244, L.286, S.287, G.289, S.290, V.291, K.292, L.316, F.390, F.391 Ligands: HEM.1, QRP.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Q.75, A:E.76, A:T.244, A:L.286, A:V.291, A:F.390, A:F.391 Hydrogen bonds: A:S.287, A:S.287, A:G.289 Water bridges: A:S.287, A:S.287, A:K.292, A:E.317, A:E.317 QRP.3: 11 residues within 4Å: Chain A: Q.68, L.80, I.90, L.175, L.236, V.239, A.240, K.292, F.391 Ligands: HEM.1, QRP.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.80, A:L.175, A:L.236, A:F.391 Hydrogen bonds: A:Q.68 Water bridges: A:Q.68, A:K.292, A:K.292, A:H.349, A:H.349

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

EDO.4: 5 residues within 4Å: Chain A: A.5, T.6, L.7, C.33, P.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.5, A:L.7, A:P.34 EDO.5: 5 residues within 4Å: Chain A: P.34, P.43, L.44, W.45, E.310 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.43, A:V.311

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
B

NzeB

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