SMTL ID : 5awv.1

Crystal structure of glycopeptide hexose oxidase DBV29 complexed with teicoplanin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-tetramer

Ligands

8 x GHP- 3MY- 3FG- GHP- GHP- OMY- 3FG: TEICOPLANIN(Non-covalent)

GHP-3MY-3FG-GHP-GHP-OMY-3FG.1: 8 residues within 4Å: Chain B: R.202, H.207, D.208, A.413, R.501, K.504 Ligands: MAN.18, NAG.19 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.202, B:D.208 Hydrogen bonds: B:H.207, B:R.501, B:R.501 Water bridges: B:D.208, B:A.413 GHP-3MY-3FG-GHP-GHP-OMY-3FG.2: 7 residues within 4Å: Chain C: S.268, R.269, R.272, R.374, D.377 Ligands: MAN.20, NAG.21 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.272, C:R.374, C:D.377 Water bridges: C:R.269 Salt bridges: C:R.269 pi-Cation interactions: C:R.272 GHP-3MY-3FG-GHP-GHP-OMY-3FG.3: 20 residues within 4Å: Chain A: V.150, C.151, T.254, W.292, Q.294, M.296, G.305, E.306, P.312, S.353, R.357, W.399 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.4, GHP-3MY-3FG-GHP-GHP-OMY-3FG.4, FAD.9, T55.22, MAN.23, NAG.24, N1L.25, MAN.26 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.306, A:P.312, A:W.399 Hydrogen bonds: A:T.254, A:E.306, A:E.306, A:E.306, A:E.306, A:S.353, A:R.357, A:R.357, A:R.357 Water bridges: A:T.254, A:S.353, A:S.353 GHP-3MY-3FG-GHP-GHP-OMY-3FG.4: 20 residues within 4Å: Chain B: V.150, C.151, T.254, W.292, Q.294, G.305, E.306, M.310, P.312, S.353, R.357, W.399 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.3, GHP-3MY-3FG-GHP-GHP-OMY-3FG.3, FAD.11, T55.12, MAN.23, MAN.26, NAG.27, N1L.28 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.150, B:E.306, B:P.312, B:W.399 Hydrogen bonds: B:T.254, B:T.254, B:E.306, B:E.306, B:E.306, B:S.353, B:R.357, B:R.357 pi-Cation interactions: B:R.357 GHP-3MY-3FG-GHP-GHP-OMY-3FG.5: 19 residues within 4Å: Chain C: V.150, C.151, T.254, W.292, Q.294, M.296, G.303, G.305, E.306, P.312, S.353, G.356, R.357, W.399 Ligands: FAD.14, T55.29, MAN.30, NAG.31, N1L.32 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.150, C:E.306, C:P.312, C:W.399 Hydrogen bonds: C:T.254, C:T.254, C:E.306, C:E.306, C:E.306, C:S.353, C:R.357, C:R.357 Water bridges: C:I.313 GHP-3MY-3FG-GHP-GHP-OMY-3FG.6: 8 residues within 4Å: Chain A: R.272, D.377 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.7, GHP-3MY-3FG-GHP-GHP-OMY-3FG.7, T55.33, MAN.34, NAG.35, N1L.36 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.272, A:R.272 Water bridges: A:R.374, A:R.374 GHP-3MY-3FG-GHP-GHP-OMY-3FG.7: 14 residues within 4Å: Chain A: E.264, R.272, D.377, R.378, Q.381 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.6, GHP-3MY-3FG-GHP-GHP-OMY-3FG.6, GHP-3MY-3FG-GHP-GHP-OMY-3FG.6, T55.33, T55.37, MAN.38, NAG.39, N1L.40, CIT.41 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.381 Hydrogen bonds: A:R.272, A:R.378, A:Q.381 pi-Cation interactions: A:R.378 GHP-3MY-3FG-GHP-GHP-OMY-3FG.8: 9 residues within 4Å: Chain B: E.438, A.439, K.440, T.443, R.446 Ligands: T55.42, MAN.43, NAG.44, N1L.45 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.439 Hydrogen bonds: B:T.443, B:R.446 Water bridges: B:T.443, B:R.446

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.9: 35 residues within 4Å: Chain A: V.86, R.87, S.88, G.89, G.90, H.91, C.92, F.93, F.96, V.97, M.108, P.127, G.149, V.150, C.151, V.154, G.155, G.157, G.158, H.159, G.164, Y.165, G.218, G.219, G.222, V.223, V.224, Y.470, N.472, Y.473, H.517 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.3, GHP-3MY-3FG-GHP-GHP-OMY-3FG.3, GHP-3MY-3FG-GHP-GHP-OMY-3FG.3, N1L.25 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:H.91, A:F.93, A:V.154 Hydrogen bonds: A:V.86, A:S.88, A:S.88, A:G.89, A:G.90, A:H.91, A:C.92, A:V.150, A:G.155, A:G.158, A:H.159, A:Y.165, A:Y.165, A:G.219, A:V.224, A:V.224, A:N.472, A:N.472, A:H.517 Water bridges: A:G.90, A:G.218 FAD.11: 33 residues within 4Å: Chain B: V.86, R.87, S.88, G.89, G.90, H.91, C.92, F.93, F.96, V.97, P.127, G.149, V.150, C.151, V.154, G.155, G.157, G.158, H.159, G.164, Y.165, G.218, G.219, G.222, V.223, V.224, Y.470, N.472, Y.473, H.517 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.4, GHP-3MY-3FG-GHP-GHP-OMY-3FG.4, N1L.28 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:H.91, B:F.93, B:V.154 Hydrogen bonds: B:V.86, B:S.88, B:S.88, B:G.89, B:G.90, B:H.91, B:C.92, B:V.150, B:G.155, B:G.155, B:G.158, B:H.159, B:Y.165, B:Y.165, B:G.219, B:V.224, B:V.224, B:Y.470, B:N.472, B:N.472, B:H.517 Water bridges: B:R.87, B:G.90, B:F.93, B:Y.473, B:Y.473 FAD.14: 34 residues within 4Å: Chain C: V.86, R.87, S.88, G.89, G.90, H.91, C.92, F.93, F.96, V.97, P.127, G.149, V.150, C.151, V.154, G.155, G.157, G.158, H.159, G.164, Y.165, G.218, G.219, G.222, V.223, V.224, Y.470, N.472, Y.473, H.517 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.5, GHP-3MY-3FG-GHP-GHP-OMY-3FG.5, GHP-3MY-3FG-GHP-GHP-OMY-3FG.5, N1L.32 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:H.91, C:F.93, C:V.154 Hydrogen bonds: C:V.86, C:S.88, C:S.88, C:G.89, C:G.90, C:H.91, C:C.92, C:V.150, C:G.155, C:G.155, C:G.158, C:H.159, C:Y.165, C:Y.165, C:G.219, C:V.224, C:V.224, C:Y.470, C:N.472, C:N.472, C:Y.473, C:H.517 Water bridges: C:F.93, C:G.218 FAD.16: 30 residues within 4Å: Chain D: V.86, R.87, S.88, G.89, G.90, H.91, C.92, F.93, F.96, V.97, P.127, G.149, V.150, C.151, V.154, G.155, G.157, G.158, H.159, G.164, Y.165, G.218, G.219, G.222, V.223, V.224, Y.470, N.472, Y.473, H.517 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:H.91, D:F.93, D:V.154 Hydrogen bonds: D:V.86, D:S.88, D:S.88, D:G.89, D:G.90, D:H.91, D:C.92, D:V.150, D:G.155, D:G.155, D:G.158, D:H.159, D:Y.165, D:Y.165, D:G.219, D:V.224, D:V.224, D:Y.470, D:N.472, D:N.472, D:H.517 Water bridges: D:G.218, D:Y.473, D:Y.473

5 x CIT: CITRIC ACID(Non-functional Binders)

CIT.10: 6 residues within 4Å: Chain A: G.81, K.82, R.83, N.513, H.514, H.516 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.81, A:H.514 Water bridges: A:R.512 Salt bridges: A:H.514, A:H.516 CIT.13: 5 residues within 4Å: Chain B: G.81, K.82, R.83, H.514, H.516 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.81 Water bridges: B:K.82, B:R.512, B:H.514, B:H.514 Salt bridges: B:H.514, B:H.516 CIT.15: 5 residues within 4Å: Chain C: G.81, K.82, R.83, H.514, H.516 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.81 Water bridges: C:K.82, C:R.512, C:R.512, C:H.514 Salt bridges: C:H.514, C:H.516 CIT.17: 8 residues within 4Å: Chain A: D.480, G.482 Chain D: T.77, G.81, K.82, R.83, H.514, H.516 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.81, A:G.482 Water bridges: D:K.82, D:R.512, D:H.514 Salt bridges: D:H.514, D:H.516 CIT.41: 5 residues within 4Å: Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.7, GHP-3MY-3FG-GHP-GHP-OMY-3FG.7, GHP-3MY-3FG-GHP-GHP-OMY-3FG.7, GHP-3MY-3FG-GHP-GHP-OMY-3FG.7, GHP-3MY-3FG-GHP-GHP-OMY-3FG.7 No protein-ligand interaction detected (PLIP)

6 x T55: 8-METHYLNONANOIC ACID(Non-covalent)(Non-functional Binders)

T55.12: 9 residues within 4Å: Chain B: M.304, P.362, D.394, Y.395, G.431, W.432 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.4, GHP-3MY-3FG-GHP-GHP-OMY-3FG.4, N1L.28 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.362, B:D.394 T55.22: 9 residues within 4Å: Chain A: M.304, P.362, D.394, Y.395, G.431, W.432 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.3, GHP-3MY-3FG-GHP-GHP-OMY-3FG.3, N1L.25 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.362, A:D.394, A:Y.395 T55.29: 9 residues within 4Å: Chain C: M.304, P.362, D.394, Y.395, G.431, W.432 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.5, GHP-3MY-3FG-GHP-GHP-OMY-3FG.5, N1L.32 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.362, C:D.394, C:Y.395 T55.33: 8 residues within 4Å: Chain A: E.264, A.265, S.268, R.269 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.6, GHP-3MY-3FG-GHP-GHP-OMY-3FG.6, GHP-3MY-3FG-GHP-GHP-OMY-3FG.7, N1L.36 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.265 T55.37: 4 residues within 4Å: Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.7, GHP-3MY-3FG-GHP-GHP-OMY-3FG.7, NAG.39, N1L.40 No protein-ligand interaction detected (PLIP) T55.42: 3 residues within 4Å: Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.8, GHP-3MY-3FG-GHP-GHP-OMY-3FG.8, N1L.45 No protein-ligand interaction detected (PLIP)

8 x MAN: alpha-D-mannopyranose(Non-functional Binders)(Non-covalent)

MAN.18: 4 residues within 4Å: Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.1, GHP-3MY-3FG-GHP-GHP-OMY-3FG.1, GHP-3MY-3FG-GHP-GHP-OMY-3FG.1, GHP-3MY-3FG-GHP-GHP-OMY-3FG.1 No protein-ligand interaction detected (PLIP) MAN.20: 5 residues within 4Å: Chain C: D.377, Q.381 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.2, GHP-3MY-3FG-GHP-GHP-OMY-3FG.2, GHP-3MY-3FG-GHP-GHP-OMY-3FG.2 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.377, C:D.377, C:Q.381 MAN.23: 5 residues within 4Å: Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.3, GHP-3MY-3FG-GHP-GHP-OMY-3FG.3, GHP-3MY-3FG-GHP-GHP-OMY-3FG.3, GHP-3MY-3FG-GHP-GHP-OMY-3FG.3, GHP-3MY-3FG-GHP-GHP-OMY-3FG.4 No protein-ligand interaction detected (PLIP) MAN.26: 5 residues within 4Å: Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.3, GHP-3MY-3FG-GHP-GHP-OMY-3FG.4, GHP-3MY-3FG-GHP-GHP-OMY-3FG.4, GHP-3MY-3FG-GHP-GHP-OMY-3FG.4, GHP-3MY-3FG-GHP-GHP-OMY-3FG.4 No protein-ligand interaction detected (PLIP) MAN.30: 4 residues within 4Å: Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.5, GHP-3MY-3FG-GHP-GHP-OMY-3FG.5, GHP-3MY-3FG-GHP-GHP-OMY-3FG.5, GHP-3MY-3FG-GHP-GHP-OMY-3FG.5 No protein-ligand interaction detected (PLIP) MAN.34: 4 residues within 4Å: Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.6, GHP-3MY-3FG-GHP-GHP-OMY-3FG.6, GHP-3MY-3FG-GHP-GHP-OMY-3FG.6, GHP-3MY-3FG-GHP-GHP-OMY-3FG.6 No protein-ligand interaction detected (PLIP) MAN.38: 5 residues within 4Å: Chain A: E.264, Q.381 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.7, GHP-3MY-3FG-GHP-GHP-OMY-3FG.7, GHP-3MY-3FG-GHP-GHP-OMY-3FG.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.381 Water bridges: A:E.264, A:Q.381 MAN.43: 8 residues within 4Å: Chain B: P.435, G.436, N.437, E.438, A.439 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.8, GHP-3MY-3FG-GHP-GHP-OMY-3FG.8, GHP-3MY-3FG-GHP-GHP-OMY-3FG.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.435, B:A.439 Water bridges: B:G.436, B:K.440

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)(Non-covalent)

NAG.19: 2 residues within 4Å: Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.1, GHP-3MY-3FG-GHP-GHP-OMY-3FG.1 No protein-ligand interaction detected (PLIP) NAG.21: 3 residues within 4Å: Chain C: R.269, D.335 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.2 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.269, C:R.269, C:D.335 NAG.24: 6 residues within 4Å: Chain A: R.357, G.358, G.359, R.360, G.361 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.357, A:R.360 NAG.27: 7 residues within 4Å: Chain B: R.357, G.358, G.359, R.360, G.361 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.4, GHP-3MY-3FG-GHP-GHP-OMY-3FG.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.360, B:R.360 NAG.31: 6 residues within 4Å: Chain C: R.357, G.358, G.359, R.360, G.361 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.5 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.357, C:R.360 NAG.35: 1 residues within 4Å: Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.6 No protein-ligand interaction detected (PLIP) NAG.39: 2 residues within 4Å: Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.7, T55.37 No protein-ligand interaction detected (PLIP) NAG.44: 5 residues within 4Å: Chain B: R.446, D.480, L.483 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.8, GHP-3MY-3FG-GHP-GHP-OMY-3FG.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.480

6 x N1L: 2-amino-2-deoxy-beta-D-glucopyranuronic acid(Non-covalent)(Non-functional Binders)

N1L.25: 10 residues within 4Å: Chain A: F.93, C.151, T.366, N.427, Y.473 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.3, GHP-3MY-3FG-GHP-GHP-OMY-3FG.3, GHP-3MY-3FG-GHP-GHP-OMY-3FG.3, FAD.9, T55.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.366, A:N.427 Water bridges: A:Q.294 N1L.28: 12 residues within 4Å: Chain B: F.93, C.151, T.366, W.399, N.427, I.429, Y.473 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.4, GHP-3MY-3FG-GHP-GHP-OMY-3FG.4, GHP-3MY-3FG-GHP-GHP-OMY-3FG.4, FAD.11, T55.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.427, B:Y.473 N1L.32: 11 residues within 4Å: Chain C: F.93, C.151, T.366, W.399, N.427, Y.473 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.5, GHP-3MY-3FG-GHP-GHP-OMY-3FG.5, GHP-3MY-3FG-GHP-GHP-OMY-3FG.5, FAD.14, T55.29 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.366, C:N.427, C:Y.473 Water bridges: C:T.366 N1L.36: 4 residues within 4Å: Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.6, GHP-3MY-3FG-GHP-GHP-OMY-3FG.6, GHP-3MY-3FG-GHP-GHP-OMY-3FG.6, T55.33 No protein-ligand interaction detected (PLIP) N1L.40: 6 residues within 4Å: Chain A: R.378, E.455 Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.7, GHP-3MY-3FG-GHP-GHP-OMY-3FG.7, GHP-3MY-3FG-GHP-GHP-OMY-3FG.7, T55.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.378, A:E.455 Salt bridges: A:R.378 N1L.45: 4 residues within 4Å: Ligands: GHP-3MY-3FG-GHP-GHP-OMY-3FG.8, GHP-3MY-3FG-GHP-GHP-OMY-3FG.8, GHP-3MY-3FG-GHP-GHP-OMY-3FG.8, T55.42 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y.C. et al., Interception of teicoplanin oxidation intermediates yields new antimicrobial scaffolds. Nat. Chem. Biol. (2011)

Release Date

2015-08-19

Peptides

Putative hexose oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putative hexose oxidase

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