SMTL ID : 4v1t.1

Heterocyclase in complex with substrate and Cofactor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.203, C.206, C.311, C.314 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.203, A:C.206, A:C.311, A:C.314 ZN.7: 4 residues within 4Å: Chain B: C.203, C.206, C.311, C.314 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.203, B:C.206, B:C.311, B:C.314

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 22 residues within 4Å: Chain A: R.344, T.351, K.409, Q.415, A.418, S.419, C.422, E.423, E.426, A.533, A.534, G.535, N.536, E.540, Q.544, E.548, R.636, E.640 Ligands: MG.3, MG.4, MG.5, PO4.6 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:R.344, A:R.344, A:T.351, A:Q.415, A:Q.415, A:E.423, A:E.426, A:E.426, A:A.534, A:N.536, A:Q.544, A:Q.544, A:E.548, A:E.640 Water bridges: A:K.409, A:S.419, A:S.419, A:R.427, A:R.552, A:R.636, A:R.636, A:Q.643, A:Q.643, A:Q.643 Salt bridges: A:K.409, A:K.409, A:R.636, A:R.636 pi-Cation interactions: A:R.344, A:R.344 ADP.8: 20 residues within 4Å: Chain B: R.344, T.351, K.409, Q.415, A.418, S.419, C.422, E.423, E.426, A.533, A.534, N.536, Q.544, E.548, R.636, E.640 Ligands: MG.9, MG.10, MG.11, PO4.12 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:R.344, B:R.344, B:Q.415, B:Q.415, B:E.426, B:A.534, B:N.536 Water bridges: B:S.419, B:S.419, B:R.427, B:R.636, B:R.636, B:R.636, B:Q.643, B:Q.643, B:Q.643 Salt bridges: B:K.409, B:K.409, B:R.636, B:R.636 pi-Cation interactions: B:R.344, B:R.344

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: K.409, R.636, E.640 Ligands: ADP.2, PO4.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.640, H2O.7, H2O.10, H2O.10 MG.4: 4 residues within 4Å: Chain A: N.532, E.548 Ligands: ADP.2, PO4.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.548, H2O.7, H2O.7, H2O.7 MG.5: 3 residues within 4Å: Chain A: E.423 Ligands: ADP.2, PO4.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.423, H2O.7, H2O.7, H2O.12 MG.9: 3 residues within 4Å: Chain B: E.423 Ligands: ADP.8, PO4.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.423, H2O.18, H2O.18, H2O.22 MG.10: 5 residues within 4Å: Chain B: K.409, E.551, E.640 Ligands: ADP.8, PO4.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.640, H2O.18, H2O.20, H2O.21 MG.11: 4 residues within 4Å: Chain B: N.532, E.548 Ligands: ADP.8, PO4.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.548, H2O.18, H2O.18, H2O.18

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 9 residues within 4Å: Chain A: E.423, R.427, E.548, R.552, E.640 Ligands: ADP.2, MG.3, MG.4, MG.5 14 PLIP interactions: 14 interactions with chain A Water bridges: A:E.423, A:E.426, A:R.427, A:R.427, A:E.548, A:E.548, A:R.552, A:R.552, A:R.552, A:E.640, A:Q.643, A:Q.643 Salt bridges: A:R.427, A:R.552 PO4.12: 9 residues within 4Å: Chain B: E.423, R.427, E.548, R.552, E.640 Ligands: ADP.8, MG.9, MG.10, MG.11 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.427, B:R.427, B:R.552, B:R.636 Salt bridges: B:R.427, B:R.552

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koehnke, J. et al., Structural Analysis of Leader Peptide Binding Enables Leader-Free Cyanobactin Processing. Nat.Chem.Biol. (2015)

Release Date

2015-01-14

Peptides

LYND: AB
PATE: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

LYND

PATE

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