SMTL ID : 6xak.1 (1 other biounit)

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

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: 23 residues within 4Å: Chain A: I.90, L.155, L.236, 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, I.361 Ligands: QRP.2, UYM.3 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:I.90, A:L.155, A:L.236, 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, A:I.361 Water bridges: A:S.64, A:S.64, A:K.292, A:R.293, A:R.293 Salt bridges: A:R.293, A:H.349 Metal complexes: A:C.351

1 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, F.177, T.244, S.287, G.289, S.290, V.291, K.292, L.316, F.390, F.391 Ligands: HEM.1, UYM.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Q.75, A:E.76, A:F.177, A:T.244, A:V.291, A:F.390 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 pi-Stacking: A:F.391

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

UYM.3: 11 residues within 4Å: Chain A: Q.68, L.80, I.90, E.232, S.235, L.236, V.239, K.292, F.391 Ligands: HEM.1, QRP.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.80, A:V.239, A:F.391, A:F.391 Hydrogen bonds: A:Q.68, A:L.80 Water bridges: A:S.64, A:S.64, A:Q.68, A:K.292, A:K.292, A:H.349

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

EDO.4: 4 residues within 4Å: Chain A: W.45, G.303, V.304, R.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.303, A:R.305 EDO.5: 2 residues within 4Å: Chain A: D.137, A.140 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.137, A:A.140

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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