SMTL ID : 5wxi.1

EarP bound with dTDP-rhamnose (soaked)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x TRH: 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE(Non-covalent)

TRH.1: 20 residues within 4Å: Chain A: I.15, F.18, G.19, D.20, L.52, Y.115, F.185, Y.187, A.211, F.249, V.250, P.251, Q.252, F.255, R.268, G.269, E.270, D.271, S.272, Y.288 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.15, A:F.185, A:A.211, A:F.249, A:F.255, A:Y.288 Hydrogen bonds: A:D.20, A:D.20, A:Y.187, A:V.250, A:V.250, A:Q.252, A:E.270, A:D.271, A:S.272 Water bridges: A:G.19, A:D.20, A:I.21, A:G.22, A:E.270, A:K.298 Salt bridges: A:R.268 TRH.10: 21 residues within 4Å: Chain B: I.15, D.16, F.18, D.20, G.22, L.52, Y.115, F.185, Y.187, A.211, F.249, V.250, P.251, Q.252, F.255, R.268, G.269, E.270, D.271, S.272, Y.288 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:I.15, B:F.18, B:F.185, B:A.211, B:F.249, B:F.255, B:Y.288 Hydrogen bonds: B:D.20, B:D.20, B:Y.187, B:V.250, B:V.250, B:Q.252, B:E.270, B:D.271, B:S.272 Water bridges: B:F.18, B:G.22, B:G.22, B:G.22, B:K.298, B:K.298 Salt bridges: B:R.268

6 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 8 residues within 4Å: Chain A: W.25, L.52, C.53, H.63, Q.64, P.251, Q.252, Q.253 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.252 BME.3: 2 residues within 4Å: Chain A: Y.157, C.158 No protein-ligand interaction detected (PLIP) BME.4: 5 residues within 4Å: Chain A: A.317, R.320, Q.335, E.338, C.339 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.320 BME.11: 5 residues within 4Å: Chain B: W.25, L.52, C.53, Q.64, Q.252 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.252 BME.12: 2 residues within 4Å: Chain B: Y.157, C.158 No protein-ligand interaction detected (PLIP) BME.13: 5 residues within 4Å: Chain B: A.317, R.320, Q.335, E.338, C.339 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.320, B:E.338 Water bridges: B:Q.335

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

SO4.5: 4 residues within 4Å: Chain A: H.346, Q.347, N.348, G.349 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.348, A:N.348, A:G.349 Water bridges: A:Q.345, A:H.346, A:H.346, A:Q.347 Salt bridges: A:H.346 SO4.6: 5 residues within 4Å: Chain A: V.46, R.50, P.57, D.58, V.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.57, A:D.58, A:V.59 Salt bridges: A:R.50 SO4.7: 3 residues within 4Å: Chain A: R.200, T.239, A.240 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.200, A:T.239, A:A.240 Water bridges: A:T.239 SO4.8: 5 residues within 4Å: Chain A: F.185, G.212, T.213, Q.214, R.268 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.213, A:Q.214, A:Q.214 Water bridges: A:I.215 Salt bridges: A:R.268 SO4.14: 5 residues within 4Å: Chain B: F.185, G.212, T.213, Q.214, R.268 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.213, B:Q.214, B:Q.214 Water bridges: B:I.215 Salt bridges: B:R.268 SO4.15: 4 residues within 4Å: Chain B: H.346, Q.347, N.348, G.349 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.348, B:N.348, B:G.349 Water bridges: B:H.346, B:Q.347 Salt bridges: B:H.346 SO4.16: 5 residues within 4Å: Chain B: V.46, R.50, P.57, D.58, V.59 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.58, B:D.58, B:V.59 Salt bridges: B:R.50

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: P.60, C.61, V.68, R.69, T.80 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.61, A:C.61, A:R.69, A:T.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sengoku, T. et al., Structural basis of protein arginine rhamnosylation by glycosyltransferase EarP. Nat. Chem. Biol. (2018)

Release Date

2018-02-28

Peptides

EarP: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

EarP

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