SMTL ID : 5lni.1

XenA - oxidized - Y183F variant in complex with 7-hydroxycoumarin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.13 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 21 residues within 4Å: Chain A: P.21, P.22, M.23, C.24, Q.25, Y.26, E.55, A.56, Q.98, H.177, H.180, R.230, A.300, W.301, G.302, V.323, G.324, R.325, L.328 Chain B: W.357 Ligands: 07L.2 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:M.23, A:R.325, B:W.357 Hydrogen bonds: A:P.22, A:C.24, A:A.56, A:Q.98, A:Q.98, A:H.177, A:H.180, A:R.230, A:R.230, A:W.301, A:G.302, A:G.324, A:R.325 Water bridges: A:F.303, A:G.304, A:R.325, A:A.326 Salt bridges: A:R.325 FMN.9: 21 residues within 4Å: Chain A: W.357 Chain B: P.21, P.22, M.23, C.24, Q.25, Y.26, E.55, A.56, Q.98, H.177, H.180, R.230, A.300, W.301, G.302, V.323, G.324, R.325, L.328 Ligands: 07L.10 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:M.23, B:R.325, A:W.357 Hydrogen bonds: B:P.22, B:C.24, B:A.56, B:Q.98, B:Q.98, B:H.177, B:H.180, B:R.230, B:R.230, B:W.301, B:G.302, B:G.324, B:R.325 Water bridges: B:F.303, B:G.304, B:R.325, B:A.326 Salt bridges: B:R.325

4 x 07L: 7-hydroxy-2H-chromen-2-one(Non-covalent)

07L.2: 11 residues within 4Å: Chain A: C.24, Y.26, A.56, I.65, H.177, H.180, F.182, F.268, W.301 Chain B: W.357 Ligands: FMN.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.65, A:F.182, B:W.357 Hydrogen bonds: A:H.177, A:H.180 07L.3: 8 residues within 4Å: Chain A: R.46, A.90, A.91, P.351 Chain B: M.27, N.34, D.35, W.36 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.90, B:W.36 Salt bridges: A:R.46 Water bridges: B:D.35, B:D.35, B:D.35 07L.10: 11 residues within 4Å: Chain A: W.357 Chain B: C.24, Y.26, A.56, I.65, H.177, H.180, F.182, F.268, W.301 Ligands: FMN.9 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.65, B:F.182, A:W.357 Hydrogen bonds: B:H.177, B:H.180 07L.11: 8 residues within 4Å: Chain A: M.27, N.34, D.35, W.36 Chain B: R.46, A.90, A.91, P.351 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.36, B:A.90 Water bridges: A:D.35, A:D.35, A:D.35 Salt bridges: B:R.46

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: P.67, R.110, R.124 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.110, A:R.110 Salt bridges: A:R.110, A:R.124 SO4.5: 3 residues within 4Å: Chain A: D.204, R.208, R.253 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.208, A:R.253, A:R.253 Salt bridges: A:R.208, A:R.253 SO4.6: 6 residues within 4Å: Chain A: Y.335, V.343, K.345, A.346, S.347, E.359 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.343, A:K.345, A:A.346, A:S.347 Water bridges: A:K.345, A:K.345, A:L.358 SO4.7: 2 residues within 4Å: Chain A: Y.7, R.17 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.17, A:R.17, A:D.319, A:D.319 Salt bridges: A:R.17 SO4.12: 3 residues within 4Å: Chain B: P.67, R.110, R.124 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.110, B:R.110 Salt bridges: B:R.110, B:R.124 SO4.13: 3 residues within 4Å: Chain B: D.204, R.208, R.253 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.208, B:R.253, B:R.253 Salt bridges: B:R.208, B:R.253 SO4.14: 6 residues within 4Å: Chain B: Y.335, V.343, K.345, A.346, S.347, E.359 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:V.343, B:K.345, B:A.346, B:S.347 Water bridges: B:K.345, B:K.345, B:L.358 SO4.15: 2 residues within 4Å: Chain B: Y.7, R.17 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.17, B:R.17, B:D.319, B:D.319 Salt bridges: B:R.17

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: R.290, R.291, K.294, L.295, P.296, D.319 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.290 Water bridges: A:K.255, A:R.290, A:R.290, A:D.319 GOL.16: 6 residues within 4Å: Chain B: R.290, R.291, K.294, L.295, P.296, D.319 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.290 Water bridges: B:K.255, B:R.290, B:R.290, B:D.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Werther, T. et al., Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase. Nat Commun (2017)

Release Date

2017-08-16

Peptides

NADH:flavin oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NADH:flavin oxidoreductase