SMTL ID : 7uf8.1

Structure of CtdP in complex with penicimutamide E and NADP+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 27 residues within 4Å: Chain A: G.12, T.14, G.15, Q.16, Q.17, T.37, R.38, D.39, D.59, G.60, N.61, N.79, N.80, G.81, Y.82, F.97, I.101, Q.118, V.133, K.137, A.158, S.159, W.160, Y.161, N.164, S.340 Ligands: N3L.2 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:A.158, A:Y.161 Hydrogen bonds: A:T.14, A:T.14, A:G.15, A:Q.16, A:Q.16, A:Q.17, A:Q.17, A:T.37, A:R.38, A:R.38, A:G.60, A:N.61, A:N.79, A:N.80, A:N.80, A:Y.82, A:Y.82, A:K.137, A:S.159, A:Y.161, A:Y.161, A:N.164, A:S.340, A:S.340 Salt bridges: A:R.38 pi-Stacking: A:F.97, A:F.97 pi-Cation interactions: A:R.38, A:R.38 NAP.3: 30 residues within 4Å: Chain B: G.12, A.13, T.14, G.15, Q.16, Q.17, T.37, R.38, D.39, A.58, D.59, G.60, N.61, M.66, N.79, N.80, G.81, Y.82, F.97, I.101, Q.118, V.133, K.137, A.158, S.159, W.160, Y.161, N.164, S.340 Ligands: N3L.5 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:A.158, B:Y.161 Hydrogen bonds: B:T.14, B:T.14, B:T.14, B:Q.16, B:Q.16, B:Q.17, B:Q.17, B:T.37, B:T.37, B:R.38, B:G.60, B:N.61, B:N.79, B:N.80, B:N.80, B:Y.82, B:K.137, B:Y.161, B:Y.161, B:N.164, B:N.164, B:S.340 Salt bridges: B:R.38 pi-Stacking: B:F.97, B:F.97 pi-Cation interactions: B:R.38 NAP.6: 26 residues within 4Å: Chain C: G.12, T.14, G.15, Q.16, Q.17, I.36, T.37, R.38, D.59, G.60, N.61, N.79, N.80, G.81, Y.82, F.97, I.101, Q.118, V.133, K.137, A.158, S.159, W.160, Y.161, N.164, I.167 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:Y.161, C:Y.161 Hydrogen bonds: C:T.14, C:T.14, C:T.14, C:Q.16, C:Q.17, C:Q.17, C:R.38, C:R.38, C:G.60, C:N.61, C:N.79, C:N.80, C:Y.161, C:N.164, C:N.164 Salt bridges: C:R.38 pi-Stacking: C:F.97, C:F.97 pi-Cation interactions: C:R.38 NAP.8: 29 residues within 4Å: Chain D: G.12, A.13, T.14, G.15, Q.16, Q.17, G.18, I.36, T.37, R.38, D.39, D.59, G.60, N.61, N.79, N.80, G.81, Y.82, F.97, I.101, Q.118, V.133, K.137, A.158, S.159, W.160, Y.161, N.164 Ligands: N3L.9 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:A.158, D:Y.161 Hydrogen bonds: D:T.14, D:T.14, D:T.14, D:T.14, D:Q.16, D:Q.17, D:Q.17, D:R.38, D:R.38, D:G.60, D:N.61, D:N.79, D:N.80, D:Y.82, D:Y.161, D:Y.161, D:N.164, D:N.164 Water bridges: D:N.80, D:V.133 Salt bridges: D:R.38 pi-Stacking: D:F.97, D:F.97 pi-Cation interactions: D:R.38

3 x N3L: Penicimutamide E(Non-covalent)

N3L.2: 25 residues within 4Å: Chain A: Y.82, Q.118, V.133, L.134, A.158, S.159, W.160, Y.161, N.164, I.167, S.169, F.170, E.173, F.174, Y.269, L.270, S.273, V.276, F.277, Y.280, L.287, F.288, P.342, V.344 Ligands: NAP.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.160, A:F.170, A:Y.269, A:P.342 Hydrogen bonds: A:S.273, A:S.273 pi-Stacking: A:F.174 N3L.5: 22 residues within 4Å: Chain B: Q.118, V.133, L.134, A.158, S.159, W.160, Y.161, N.164, I.167, S.169, F.170, F.174, Y.269, S.273, V.276, F.277, Y.280, L.287, F.288, P.342, V.344 Ligands: NAP.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.134, B:F.170, B:Y.269, B:V.276, B:L.287, B:P.342 Hydrogen bonds: B:S.273, B:S.273 pi-Stacking: B:F.174 N3L.9: 19 residues within 4Å: Chain D: Q.118, V.133, L.134, A.158, S.159, W.160, Y.161, N.164, I.167, S.169, F.170, F.174, Q.271, S.273, V.276, Y.280, L.287, F.288 Ligands: NAP.8 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.134, D:F.170, D:V.276 Hydrogen bonds: D:S.273, D:S.273

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

EDO.4: 8 residues within 4Å: Chain B: A.303, A.304, F.306, Q.307, E.315 Chain C: R.314, E.322 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.307, B:E.315, B:E.315 EDO.7: 5 residues within 4Å: Chain C: T.319, R.321, E.322, E.325 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.319, C:T.319, C:E.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Z. et al., An NmrA-like enzyme-catalysed redox-mediated Diels-Alder cycloaddition with anti-selectivity. Nat.Chem. (2023)

Release Date

2023-02-22

Peptides

CtdP: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CtdP