SMTL ID : 6xaj.1

Crystal structure of NzeB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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.102, L.106, 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, G.353, A.357 Ligands: EDO.4 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:I.90, A:L.102, A:L.106, A:L.155, A:L.237, A:F.248, A:L.286, A:V.291, A:L.316, A:F.344, A:P.352, A:A.357 Water bridges: A:Q.68, A:Q.68, A:R.293, A:R.348, 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.2

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

EDO.2: 2 residues within 4Å: Chain A: R.375, T.400 No protein-ligand interaction detected (PLIP) EDO.3: 8 residues within 4Å: Chain A: Q.75, E.76, F.177, S.287, G.289, S.290, K.292, F.390 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.76, A:E.76, A:S.287, A:S.287 Water bridges: A:K.292 EDO.4: 3 residues within 4Å: Chain A: T.244, F.391 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.240, A:S.287, A:S.287

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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