SMTL ID : 6f7l.1

Crystal structure of LkcE R326Q mutant in complex with its substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 33 residues within 4Å: Chain A: V.17, G.18, G.19, G.20, G.21, S.22, F.39, E.40, A.41, G.46, G.47, H.48, G.66, V.67, E.68, H.69, P.231, V.232, A.259, T.260, H.261, V.264, R.267, L.268, F.349, W.366, L.368, G.395, T.396, G.402, H.403, A.406 Ligands: CWH.4 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:H.48, A:F.349, A:W.366, A:W.366, A:L.368 Hydrogen bonds: A:G.21, A:S.22, A:S.22, A:S.22, A:A.41, A:G.46, A:H.48, A:H.48, A:E.68, A:H.69, A:H.69, A:V.232, A:V.232, A:R.267, A:T.396, A:H.403, A:H.403 Water bridges: A:G.20, A:G.23, A:E.40, A:Y.44, A:A.49, A:A.49 Salt bridges: A:H.48, A:H.261 FAD.7: 31 residues within 4Å: Chain B: V.17, G.18, G.19, G.20, G.21, S.22, F.39, E.40, A.41, G.46, G.47, H.48, G.66, V.67, E.68, H.69, P.231, V.232, T.260, H.261, V.264, L.268, F.349, W.366, L.368, G.395, T.396, G.402, H.403, A.406 Ligands: CWH.12 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:H.48, B:F.349, B:W.366, B:W.366, B:L.368 Hydrogen bonds: B:G.21, B:S.22, B:S.22, B:S.22, B:A.41, B:G.46, B:H.48, B:H.48, B:E.68, B:H.69, B:H.69, B:V.232, B:V.232, B:T.396, B:H.403, B:H.403 Water bridges: B:G.20, B:G.23, B:G.47, B:A.49, B:A.49, B:E.404 Salt bridges: B:H.48, B:H.261

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 1 residues within 4Å: Chain A: E.115 No protein-ligand interaction detected (PLIP) CA.3: 4 residues within 4Å: Chain A: N.166, E.322, Q.324 Ligands: GOL.5 No protein-ligand interaction detected (PLIP) CA.8: 2 residues within 4Å: Chain B: K.340, V.341 No protein-ligand interaction detected (PLIP)

2 x CWH: [(2~{S},5~{R},8~{S},11~{S})-1-[(2~{R},3~{R},5~{R},6~{S})-3,5-dimethyl-6-oxidanyl-4-oxidanylidene-oxan-2-yl]-5,11-dimeth yl-8-oxidanyl-13-[[(2~{S})-2-oxidanylpropanoyl]amino]tridecan-2-yl] ethanoate(Non-covalent)

CWH.4: 19 residues within 4Å: Chain A: G.66, E.68, H.69, L.74, I.171, Y.172, N.183, M.185, Y.186, L.189, W.204, Q.330, F.349, V.376, V.400, T.401, G.402, Q.432 Ligands: FAD.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:E.68, A:Y.172, A:Y.172, A:M.185, A:Y.186, A:Y.186, A:L.189, A:W.204, A:F.349, A:V.376, A:T.401 Hydrogen bonds: A:E.68, A:H.69, A:N.183, A:Q.330, A:T.401, A:Q.432 Salt bridges: A:K.379 CWH.12: 18 residues within 4Å: Chain B: E.68, H.69, L.74, I.171, Y.172, N.183, M.185, Y.186, L.189, W.204, Q.330, F.349, V.376, V.400, T.401, G.402, Q.432 Ligands: FAD.7 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.74, B:Y.172, B:Y.172, B:Y.186, B:L.189, B:W.204, B:V.376, B:T.401 Hydrogen bonds: B:N.183, B:Y.186, B:Q.330, B:T.401, B:Q.432 Water bridges: B:G.66, B:E.68, B:H.403, B:G.405

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 11 residues within 4Å: Chain A: N.166, P.167, S.170, G.174, C.175, A.177, S.179, F.310, M.325, G.326 Ligands: CA.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.170, A:S.179, A:S.179, A:G.326 GOL.6: 9 residues within 4Å: Chain A: H.128, N.132, F.191, S.192, N.194 Chain B: K.73, M.193, N.194, Y.203 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.73, B:N.194, A:H.128, A:N.132 Water bridges: B:N.71, B:M.193, A:N.194 GOL.13: 9 residues within 4Å: Chain A: N.194, Y.203 Chain B: H.128, N.132, F.191, S.192, N.194, S.197, S.200 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.128, B:N.132, B:S.197, B:S.200, A:N.194 GOL.14: 4 residues within 4Å: Chain B: E.296, V.341, S.342, P.344 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.333 Water bridges: B:N.333, B:N.333 GOL.15: 4 residues within 4Å: Chain B: G.86, I.87, G.88, Q.208 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.88 GOL.16: 2 residues within 4Å: Chain B: R.217, S.220 4 PLIP interactions: 4 interactions with chain B Water bridges: B:S.213, B:R.217, B:R.217, B:S.220 GOL.17: 7 residues within 4Å: Chain A: H.121, E.122, D.125 Chain B: T.89, Y.90, Q.208, H.336 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:H.121, A:E.122, A:D.125, B:Q.208, B:H.336 Water bridges: A:E.122, A:D.125, B:T.89, B:T.89, B:V.91, B:R.205

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 3 residues within 4Å: Chain B: V.54, E.55, I.361 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.55 Hydrogen bonds: B:E.55 Water bridges: B:Q.294, B:Q.294 ACT.10: 5 residues within 4Å: Chain B: Q.294, E.358, R.359, V.360, I.361 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.361 ACT.11: 5 residues within 4Å: Chain B: H.97, N.108, L.110, A.302, G.303 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.302 Salt bridges: B:H.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dorival, J. et al., Insights into a dual function amide oxidase/macrocyclase from lankacidin biosynthesis. Nat Commun (2018)

Release Date

2018-09-19

Peptides

Amine oxidase LkcE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Amine oxidase LkcE