SMTL ID : 1g5q.1

EPID H67N COMPLEXED WITH SUBSTRATE PEPTIDE DSYTC

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

homo-12-mer

Ligands

12 x ASP- SER- TYR- THR- CYS: LANTIBIOTIC EPIDERMIN(Non-covalent)

ASP-SER-TYR-THR-CYS.1: 22 residues within 4Å: Chain A: I.13, N.14, I.16, N.17, N.117, S.148, F.149, E.150, I.151, S.152, Y.156, N.159, I.160, T.161, M.162 Chain B: N.19, H.20, V.23, F.52 Chain E: N.66, I.68 Ligands: FMN.5 22 PLIP interactions: 17 interactions with chain A, 4 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: A:I.13, A:I.16, A:F.149, B:V.23, B:F.52 Hydrogen bonds: A:N.14, A:N.14, A:N.117, A:N.117, A:N.117, A:S.148, A:F.149, A:F.149, A:I.151, A:S.152, A:S.152, A:Y.156, A:M.162, A:M.162, B:N.19, B:H.20, E:N.66 ASP-SER-TYR-THR-CYS.2: 22 residues within 4Å: Chain A: N.19, H.20, V.23, F.52 Chain B: I.13, N.14, I.16, N.17, N.117, S.148, F.149, E.150, I.151, S.152, Y.156, N.159, I.160, T.161, M.162 Chain L: N.66, I.68 Ligands: FMN.7 20 PLIP interactions: 4 interactions with chain A, 15 interactions with chain B, 1 interactions with chain L Hydrophobic interactions: A:V.23, A:F.52, B:I.13, B:I.16, B:F.149 Hydrogen bonds: A:N.19, A:H.20, B:N.14, B:N.14, B:N.117, B:N.117, B:N.117, B:S.148, B:F.149, B:F.149, B:I.151, B:S.152, B:M.162, B:M.162, L:N.66 ASP-SER-TYR-THR-CYS.3: 21 residues within 4Å: Chain C: I.13, N.14, I.16, N.17, N.117, S.148, F.149, E.150, I.151, S.152, N.159, I.160, T.161, M.162 Chain J: N.66, I.68 Chain L: N.19, H.20, V.23, F.52 Ligands: FMN.8 20 PLIP interactions: 15 interactions with chain C, 1 interactions with chain J, 4 interactions with chain L Hydrophobic interactions: C:I.13, C:I.16, C:F.149, C:N.159, L:V.23 Hydrogen bonds: C:N.14, C:N.14, C:N.117, C:N.117, C:S.148, C:F.149, C:F.149, C:I.151, C:S.152, C:M.162, J:N.66, L:N.19, L:H.20 Water bridges: C:N.115 pi-Stacking: L:F.52 ASP-SER-TYR-THR-CYS.4: 22 residues within 4Å: Chain D: I.13, N.14, I.16, N.17, N.117, S.148, F.149, E.150, I.151, S.152, Y.156, N.159, I.160, T.161, M.162 Chain G: N.19, H.20, V.23, F.52 Chain K: N.66, I.68 Ligands: FMN.10 22 PLIP interactions: 17 interactions with chain D, 1 interactions with chain K, 4 interactions with chain G Hydrophobic interactions: D:I.13, D:I.16, D:F.149, D:N.159, G:V.23 Hydrogen bonds: D:N.14, D:N.14, D:N.117, D:N.117, D:N.117, D:S.148, D:F.149, D:F.149, D:F.149, D:I.151, D:S.152, D:M.162, K:N.66, G:N.19, G:N.19 Water bridges: D:N.115 pi-Stacking: G:F.52 ASP-SER-TYR-THR-CYS.11: 22 residues within 4Å: Chain E: I.13, N.14, I.16, N.17, N.117, S.148, F.149, E.150, I.151, S.152, Y.156, N.159, I.160, T.161, M.162 Chain F: N.19, H.20, V.23, F.52 Chain I: N.66, I.68 Ligands: FMN.15 21 PLIP interactions: 4 interactions with chain F, 16 interactions with chain E, 1 interactions with chain I Hydrophobic interactions: F:V.23, F:F.52, E:I.13, E:I.16, E:F.149 Hydrogen bonds: F:N.19, F:N.19, E:N.14, E:N.14, E:N.117, E:N.117, E:N.117, E:S.148, E:F.149, E:F.149, E:I.151, E:S.152, E:S.152, E:M.162, E:M.162, I:N.66 ASP-SER-TYR-THR-CYS.12: 22 residues within 4Å: Chain D: N.66, I.68 Chain E: N.19, H.20, V.23, F.52 Chain F: I.13, N.14, I.16, N.17, N.117, S.148, F.149, E.150, I.151, S.152, Y.156, N.159, I.160, T.161, M.162 Ligands: FMN.17 21 PLIP interactions: 16 interactions with chain F, 4 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: F:I.13, F:I.16, F:F.149, E:V.23, E:F.52 Hydrogen bonds: F:N.14, F:N.14, F:N.117, F:N.117, F:S.148, F:S.148, F:F.149, F:F.149, F:I.151, F:S.152, F:Y.156, F:M.162, F:M.162, E:N.19, E:H.20, D:N.66 ASP-SER-TYR-THR-CYS.13: 21 residues within 4Å: Chain B: N.66, I.68 Chain D: N.19, H.20, V.23, F.52 Chain G: I.13, N.14, I.16, N.17, N.117, S.148, F.149, E.150, I.151, S.152, N.159, I.160, T.161, M.162 Ligands: FMN.18 22 PLIP interactions: 17 interactions with chain G, 1 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: G:I.13, G:I.16, G:F.149, G:N.159, D:V.23 Hydrogen bonds: G:N.14, G:N.14, G:N.17, G:N.117, G:N.117, G:N.117, G:S.148, G:F.149, G:F.149, G:I.151, G:S.152, G:M.162, B:N.66, D:N.19, D:H.20 Water bridges: G:N.115 pi-Stacking: D:F.52 ASP-SER-TYR-THR-CYS.14: 22 residues within 4Å: Chain C: N.66, I.68 Chain H: I.13, N.14, I.16, N.17, N.117, S.148, F.149, E.150, I.151, S.152, Y.156, N.159, I.160, T.161, M.162 Chain K: N.19, H.20, V.23, F.52 Ligands: FMN.20 22 PLIP interactions: 16 interactions with chain H, 4 interactions with chain K, 2 interactions with chain C Hydrophobic interactions: H:I.13, H:I.16, H:F.149, H:N.159, K:V.23 Hydrogen bonds: H:N.14, H:N.14, H:N.117, H:N.117, H:S.148, H:F.149, H:F.149, H:I.151, H:S.152, H:Y.156, H:M.162, K:N.19, K:N.19, C:N.66, C:N.66 Water bridges: H:N.115 pi-Stacking: K:F.52 ASP-SER-TYR-THR-CYS.21: 22 residues within 4Å: Chain A: N.66, I.68 Chain I: I.13, N.14, I.16, N.17, N.117, S.148, F.149, E.150, I.151, S.152, Y.156, N.159, I.160, T.161, M.162 Chain J: N.19, H.20, V.23, F.52 Ligands: FMN.25 21 PLIP interactions: 16 interactions with chain I, 1 interactions with chain A, 4 interactions with chain J Hydrophobic interactions: I:I.13, I:I.16, I:F.149, J:V.23, J:F.52 Hydrogen bonds: I:N.14, I:N.14, I:N.117, I:N.117, I:N.117, I:S.148, I:F.149, I:F.149, I:I.151, I:S.152, I:S.152, I:M.162, I:M.162, A:N.66, J:N.19, J:H.20 ASP-SER-TYR-THR-CYS.22: 22 residues within 4Å: Chain H: N.66, I.68 Chain I: N.19, H.20, V.23, F.52 Chain J: I.13, N.14, I.16, N.17, N.117, S.148, F.149, E.150, I.151, S.152, Y.156, N.159, I.160, T.161, M.162 Ligands: FMN.27 20 PLIP interactions: 4 interactions with chain I, 15 interactions with chain J, 1 interactions with chain H Hydrophobic interactions: I:V.23, I:F.52, J:I.13, J:I.16, J:F.149 Hydrogen bonds: I:N.19, I:N.19, J:N.14, J:N.14, J:N.117, J:N.117, J:S.148, J:F.149, J:F.149, J:I.151, J:S.152, J:Y.156, J:M.162, J:M.162, H:N.66 ASP-SER-TYR-THR-CYS.23: 21 residues within 4Å: Chain F: N.66, I.68 Chain H: N.19, H.20, V.23, F.52 Chain K: I.13, N.14, I.16, N.17, N.117, S.148, F.149, E.150, I.151, S.152, N.159, I.160, T.161, M.162 Ligands: FMN.28 20 PLIP interactions: 15 interactions with chain K, 1 interactions with chain F, 4 interactions with chain H Hydrophobic interactions: K:I.13, K:I.16, K:F.149, K:N.159, H:V.23 Hydrogen bonds: K:N.14, K:N.14, K:N.117, K:N.117, K:S.148, K:F.149, K:F.149, K:I.151, K:S.152, K:M.162, F:N.66, H:N.19, H:H.20 Water bridges: K:N.115 pi-Stacking: H:F.52 ASP-SER-TYR-THR-CYS.24: 22 residues within 4Å: Chain C: N.19, H.20, V.23, F.52 Chain G: N.66, I.68 Chain L: I.13, N.14, I.16, N.17, N.117, S.148, F.149, E.150, I.151, S.152, Y.156, N.159, I.160, T.161, M.162 Ligands: FMN.30 23 PLIP interactions: 17 interactions with chain L, 5 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: L:I.13, L:I.16, L:F.149, L:N.159, C:V.23 Hydrogen bonds: L:N.14, L:N.14, L:N.117, L:N.117, L:N.117, L:S.148, L:F.149, L:F.149, L:F.149, L:I.151, L:S.152, L:M.162, C:N.19, C:N.19, C:H.20, G:N.66 Water bridges: L:N.115 pi-Stacking: C:F.52

12 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.5: 23 residues within 4Å: Chain A: T.10, A.11, S.12, I.13, S.37, S.39, F.43, S.83, A.84, N.85, T.86, N.115, M.116, M.120 Chain B: L.51 Chain E: P.63, L.64, L.65, N.67, C.95, D.96, T.101 Ligands: ASP-SER-TYR-THR-CYS.1 21 PLIP interactions: 19 interactions with chain A, 1 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: A:I.13, A:F.43, A:F.43, B:L.51 Hydrogen bonds: A:A.11, A:A.11, A:I.13, A:S.37, A:S.39, A:S.83, A:S.83, A:A.84, A:N.85, A:T.86, A:N.115, E:T.101 Water bridges: A:S.39, A:N.85, A:N.97, A:N.97 pi-Stacking: A:F.43 FMN.7: 22 residues within 4Å: Chain A: L.51 Chain B: T.10, A.11, S.12, I.13, S.37, S.39, F.43, S.83, A.84, N.85, T.86, N.115, M.116, M.120 Chain L: P.63, L.64, L.65, C.95, D.96, T.101 Ligands: ASP-SER-TYR-THR-CYS.2 22 PLIP interactions: 20 interactions with chain B, 1 interactions with chain L, 1 interactions with chain A Hydrophobic interactions: B:I.13, B:F.43, B:F.43, A:L.51 Hydrogen bonds: B:A.11, B:A.11, B:I.13, B:S.37, B:S.39, B:S.83, B:S.83, B:A.84, B:N.85, B:T.86, B:T.86, B:N.115, L:T.101 Water bridges: B:S.39, B:N.85, B:N.97, B:N.97 pi-Stacking: B:F.43 FMN.8: 23 residues within 4Å: Chain C: T.10, A.11, S.12, I.13, S.37, S.39, F.43, S.83, A.84, N.85, T.86, N.115, M.116, M.120 Chain J: P.63, L.64, L.65, N.67, C.95, D.96, T.101 Chain L: L.51 Ligands: ASP-SER-TYR-THR-CYS.3 19 PLIP interactions: 16 interactions with chain C, 1 interactions with chain L, 2 interactions with chain J Hydrophobic interactions: C:I.13, C:F.43, L:L.51 Hydrogen bonds: C:A.11, C:A.11, C:I.13, C:S.37, C:S.39, C:S.83, C:S.83, C:A.84, C:N.85, C:T.86, C:N.115, J:T.101 Water bridges: C:N.85, C:N.97, J:N.67 pi-Stacking: C:F.43 FMN.10: 23 residues within 4Å: Chain D: T.10, A.11, S.12, I.13, S.37, S.39, F.43, S.83, A.84, N.85, T.86, N.115, M.116, M.120 Chain G: L.51 Chain K: P.63, L.64, L.65, C.95, D.96, N.97, T.101 Ligands: ASP-SER-TYR-THR-CYS.4 21 PLIP interactions: 19 interactions with chain D, 1 interactions with chain G, 1 interactions with chain K Hydrophobic interactions: D:I.13, D:F.43, G:L.51 Hydrogen bonds: D:A.11, D:A.11, D:I.13, D:S.37, D:S.39, D:S.83, D:S.83, D:A.84, D:N.85, D:T.86, D:T.86, D:N.115, K:T.101 Water bridges: D:N.85, D:N.97, D:N.97, D:N.97 pi-Stacking: D:F.43 FMN.15: 23 residues within 4Å: Chain E: T.10, A.11, S.12, I.13, S.37, S.39, F.43, S.83, A.84, N.85, T.86, N.115, M.116, M.120 Chain F: L.51 Chain I: P.63, L.64, L.65, N.67, C.95, D.96, T.101 Ligands: ASP-SER-TYR-THR-CYS.11 23 PLIP interactions: 20 interactions with chain E, 2 interactions with chain I, 1 interactions with chain F Hydrophobic interactions: E:I.13, E:F.43, E:F.43, F:L.51 Hydrogen bonds: E:A.11, E:A.11, E:I.13, E:S.37, E:S.39, E:S.83, E:S.83, E:A.84, E:N.85, E:T.86, E:T.86, E:N.115, I:T.101, I:T.101 Water bridges: E:S.39, E:N.85, E:N.97, E:N.97 pi-Stacking: E:F.43 FMN.17: 22 residues within 4Å: Chain D: P.63, L.64, L.65, C.95, D.96, T.101 Chain E: L.51 Chain F: T.10, A.11, S.12, I.13, S.37, S.39, F.43, S.83, A.84, N.85, T.86, N.115, M.116, M.120 Ligands: ASP-SER-TYR-THR-CYS.12 21 PLIP interactions: 19 interactions with chain F, 1 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: F:I.13, F:F.43, F:F.43, E:L.51 Hydrogen bonds: F:A.11, F:A.11, F:I.13, F:S.37, F:S.39, F:S.83, F:S.83, F:A.84, F:N.85, F:T.86, F:N.115, D:T.101 Water bridges: F:S.39, F:N.85, F:N.97, F:N.97 pi-Stacking: F:F.43 FMN.18: 23 residues within 4Å: Chain B: P.63, L.64, L.65, N.67, C.95, D.96, T.101 Chain D: L.51 Chain G: T.10, A.11, S.12, I.13, S.37, S.39, F.43, S.83, A.84, N.85, T.86, N.115, M.116, M.120 Ligands: ASP-SER-TYR-THR-CYS.13 20 PLIP interactions: 3 interactions with chain B, 16 interactions with chain G, 1 interactions with chain D Hydrogen bonds: B:T.101, B:T.101, G:A.11, G:A.11, G:I.13, G:S.37, G:S.39, G:S.83, G:S.83, G:A.84, G:N.85, G:T.86, G:N.115 Water bridges: B:N.67, G:N.85, G:N.97 Hydrophobic interactions: G:I.13, G:F.43, D:L.51 pi-Stacking: G:F.43 FMN.20: 23 residues within 4Å: Chain C: P.63, L.64, L.65, C.95, D.96, N.97, T.101 Chain H: T.10, A.11, S.12, I.13, S.37, S.39, F.43, S.83, A.84, N.85, T.86, N.115, M.116, M.120 Chain K: L.51 Ligands: ASP-SER-TYR-THR-CYS.14 22 PLIP interactions: 19 interactions with chain H, 1 interactions with chain K, 2 interactions with chain C Hydrophobic interactions: H:I.13, H:F.43, K:L.51 Hydrogen bonds: H:A.11, H:A.11, H:I.13, H:S.37, H:S.39, H:S.83, H:S.83, H:A.84, H:N.85, H:T.86, H:T.86, H:N.115, C:T.101, C:T.101 Water bridges: H:N.85, H:N.97, H:N.97, H:N.97 pi-Stacking: H:F.43 FMN.25: 23 residues within 4Å: Chain A: P.63, L.64, L.65, N.67, C.95, D.96, T.101 Chain I: T.10, A.11, S.12, I.13, S.37, S.39, F.43, S.83, A.84, N.85, T.86, N.115, M.116, M.120 Chain J: L.51 Ligands: ASP-SER-TYR-THR-CYS.21 22 PLIP interactions: 19 interactions with chain I, 2 interactions with chain A, 1 interactions with chain J Hydrophobic interactions: I:I.13, I:F.43, I:F.43, J:L.51 Hydrogen bonds: I:A.11, I:A.11, I:I.13, I:S.37, I:S.39, I:S.83, I:S.83, I:A.84, I:N.85, I:T.86, I:N.115, A:T.101, A:T.101 Water bridges: I:S.39, I:N.85, I:N.97, I:N.97 pi-Stacking: I:F.43 FMN.27: 22 residues within 4Å: Chain H: P.63, L.64, L.65, C.95, D.96, T.101 Chain I: L.51 Chain J: T.10, A.11, S.12, I.13, S.37, S.39, F.43, S.83, A.84, N.85, T.86, N.115, M.116, M.120 Ligands: ASP-SER-TYR-THR-CYS.22 22 PLIP interactions: 20 interactions with chain J, 1 interactions with chain I, 1 interactions with chain H Hydrophobic interactions: J:I.13, J:F.43, J:F.43, I:L.51 Hydrogen bonds: J:A.11, J:A.11, J:I.13, J:S.37, J:S.39, J:S.83, J:S.83, J:A.84, J:N.85, J:T.86, J:T.86, J:N.115, H:T.101 Water bridges: J:S.39, J:N.85, J:N.97, J:N.97 pi-Stacking: J:F.43 FMN.28: 23 residues within 4Å: Chain F: P.63, L.64, L.65, N.67, C.95, D.96, T.101 Chain H: L.51 Chain K: T.10, A.11, S.12, I.13, S.37, S.39, F.43, S.83, A.84, N.85, T.86, N.115, M.116, M.120 Ligands: ASP-SER-TYR-THR-CYS.23 20 PLIP interactions: 16 interactions with chain K, 3 interactions with chain F, 1 interactions with chain H Hydrophobic interactions: K:I.13, K:F.43, H:L.51 Hydrogen bonds: K:A.11, K:A.11, K:I.13, K:S.37, K:S.39, K:S.83, K:S.83, K:A.84, K:N.85, K:T.86, K:N.115, F:T.101, F:T.101 Water bridges: K:N.85, K:N.97, F:N.67 pi-Stacking: K:F.43 FMN.30: 23 residues within 4Å: Chain C: L.51 Chain G: P.63, L.64, L.65, C.95, D.96, N.97, T.101 Chain L: T.10, A.11, S.12, I.13, S.37, S.39, F.43, S.83, A.84, N.85, T.86, N.115, M.116, M.120 Ligands: ASP-SER-TYR-THR-CYS.24 21 PLIP interactions: 18 interactions with chain L, 2 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: L:I.13, L:F.43, C:L.51 Hydrogen bonds: L:A.11, L:A.11, L:I.13, L:S.37, L:S.39, L:S.83, L:S.83, L:A.84, L:N.85, L:T.86, L:N.115, G:T.101, G:T.101 Water bridges: L:N.85, L:N.97, L:N.97, L:N.97 pi-Stacking: L:F.43

6 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 8 residues within 4Å: Chain A: K.89, D.96 Chain E: K.89, D.96 Chain I: K.89, D.96 Ligands: TRS.16, TRS.26 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 3 interactions with chain I Hydrogen bonds: A:K.89, E:K.89, I:K.89, I:D.96, I:D.96 TRS.9: 6 residues within 4Å: Chain C: K.89, D.96 Chain H: K.89, D.96 Chain J: K.89, D.96 10 PLIP interactions: 3 interactions with chain J, 2 interactions with chain C, 5 interactions with chain H Hydrogen bonds: J:K.89, C:K.89, C:D.96, H:K.89, H:D.96, H:D.96 Water bridges: J:K.89, J:N.97, H:K.89, H:N.97 TRS.16: 8 residues within 4Å: Chain A: K.89, D.96 Chain E: K.89, D.96 Chain I: K.89, D.96 Ligands: TRS.6, TRS.26 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E, 2 interactions with chain I Hydrogen bonds: A:K.89, A:D.96, E:K.89, I:K.89, I:D.96 TRS.19: 6 residues within 4Å: Chain B: K.89, D.96 Chain G: K.89, D.96 Chain L: K.89, D.96 10 PLIP interactions: 5 interactions with chain L, 3 interactions with chain B, 2 interactions with chain G Hydrogen bonds: L:K.89, L:D.96, L:D.96, B:K.89, G:K.89, G:D.96 Water bridges: L:K.89, L:N.97, B:K.89, B:N.97 TRS.26: 8 residues within 4Å: Chain A: K.89, D.96 Chain E: K.89, D.96 Chain I: K.89, D.96 Ligands: TRS.6, TRS.16 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E, 2 interactions with chain I Hydrogen bonds: A:K.89, E:K.89, E:D.96, I:K.89, I:D.96 TRS.29: 6 residues within 4Å: Chain D: K.89, D.96 Chain F: K.89, D.96 Chain K: K.89, D.96 9 PLIP interactions: 4 interactions with chain D, 3 interactions with chain F, 2 interactions with chain K Hydrogen bonds: D:K.89, D:D.96, F:K.89, K:K.89, K:D.96 Water bridges: D:K.89, D:N.97, F:K.89, F:N.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blaesse, M. et al., Crystal structure of the peptidyl-cysteine decarboxylase EpiD complexed with a pentapeptide substrate. EMBO J. (2000)

Release Date

2001-05-02

Peptides

EPIDERMIN MODIFYING ENZYME EPID: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
G

D
L

E
A

F
D

G
G

H
L

I
A

J
D

K
G

L
L

EPIDERMIN MODIFYING ENZYME EPID