SMTL ID : 5f5n.1

The structure of monooxygenase KstA11 in complex with NAD and its substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 25 residues within 4Å: Chain A: G.8, A.9, T.10, G.11, T.12, Q.13, R.33, D.54, L.55, N.56, V.74, Q.75, T.76, F.77, E.86, Q.89, S.109, V.110, K.125, P.144, T.145, F.146, F.147, N.150 Ligands: 5VD.2 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:V.110, A:P.144 Hydrogen bonds: A:G.8, A:T.10, A:T.10, A:T.12, A:Q.13, A:Q.13, A:R.33, A:R.33, A:D.54, A:L.55, A:Q.75, A:Q.89, A:K.125, A:F.147, A:N.150, A:N.150 Water bridges: A:A.9, A:T.10, A:T.12, A:T.12, A:T.12, A:G.14, A:R.33, A:N.56, A:Q.75 pi-Stacking: A:F.147 pi-Cation interactions: A:R.33, A:R.33 NAD.8: 25 residues within 4Å: Chain B: G.8, A.9, T.10, G.11, T.12, Q.13, R.33, D.54, L.55, N.56, V.74, Q.75, T.76, F.77, E.86, Q.89, V.110, K.125, P.144, T.145, F.146, F.147, N.150 Ligands: 5VD.9, GOL.10 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:V.110, B:P.144 Hydrogen bonds: B:G.8, B:T.10, B:T.10, B:T.12, B:Q.13, B:Q.13, B:R.33, B:D.54, B:L.55, B:Q.75, B:Q.89, B:K.125, B:F.147, B:N.150, B:N.150 Water bridges: B:A.9, B:T.12, B:T.12, B:G.14, B:R.33, B:R.33, B:Q.75, B:T.76 pi-Stacking: B:F.147 pi-Cation interactions: B:R.33

2 x 5VD: methyl (1~{R},2~{R},4~{S})-2-methyl-2,4,5,7,10-pentakis(oxidanyl)-6,11-bis(oxidanylidene)-3,4-dihydro-1~{H}-tetracene-1-carboxylate(Non-covalent)

5VD.2: 17 residues within 4Å: Chain A: F.77, M.78, V.110, H.121, F.146, N.150, F.151, W.154, L.167, I.242, I.248, M.251, F.252, F.255, Y.260 Ligands: NAD.1, GOL.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.110, A:W.154, A:W.154, A:I.248 Hydrogen bonds: A:N.150, A:Y.260 Water bridges: A:P.243 5VD.9: 17 residues within 4Å: Chain B: F.77, M.78, V.110, H.121, F.146, N.150, F.151, W.154, L.167, I.242, I.248, M.251, F.252, F.255, Y.260 Ligands: NAD.8, GOL.10 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.110, B:W.154, B:W.154, B:I.248 Hydrogen bonds: B:N.150, B:Y.260

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: T.173, R.174, F.255, Q.256, T.257, D.258 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.174, A:T.257 Water bridges: A:Q.172, A:R.174, A:Y.260 GOL.4: 4 residues within 4Å: Chain A: N.150, A.153, W.154 Ligands: 5VD.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.150 Water bridges: A:N.150 GOL.5: 3 residues within 4Å: Chain A: Q.58, A.59, R.62 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.58, A:A.59, A:R.62, A:R.62 GOL.6: 2 residues within 4Å: Chain A: D.192, D.193 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.192, A:D.193, A:D.193, A:D.193 GOL.7: 3 residues within 4Å: Chain A: R.24, V.185, H.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.24 Water bridges: A:R.24 GOL.10: 5 residues within 4Å: Chain B: N.150, A.153, W.154 Ligands: NAD.8, 5VD.9 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.149, B:N.150 GOL.11: 5 residues within 4Å: Chain B: T.173, R.174, F.255, Q.256, D.258 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.172, B:R.174, B:Q.256, B:D.258 Water bridges: B:Y.260 GOL.12: 9 residues within 4Å: Chain B: F.151, A.152, A.153, W.154, G.155, P.156, Q.157, W.286, P.289 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.152, B:A.153, B:G.155, B:P.156 GOL.13: 3 residues within 4Å: Chain B: Q.58, A.59, R.62 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.58, B:A.59, B:R.62, B:R.62 Water bridges: B:Q.58, B:Q.58 GOL.14: 2 residues within 4Å: Chain B: A.63, A.66 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.63

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.15: 3 residues within 4Å: Chain B: P.272, G.273, R.275 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.275 Salt bridges: B:R.275 EPE.16: 6 residues within 4Å: Chain B: P.27, A.44, G.47, V.48, S.49 Ligands: MG.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.44, B:G.47 Water bridges: B:T.3

1 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 4 residues within 4Å: Chain B: P.27, V.28, S.49 Ligands: EPE.16 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Hydroxyl regioisomerization of anthracycline catalyzed by a four-enzyme cascade. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2016-12-21

Peptides

Monooxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Monooxygenase