SMTL ID : 5xvr.3 (2 other biounits)

EarP bound with dTDP-rhamnose (co-crystal)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

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

TRH.1: 19 residues within 4Å: Chain A: F.20, G.21, N.22, L.54, Y.117, F.187, Y.189, A.213, F.251, V.252, P.253, Q.254, F.257, R.270, G.271, E.272, D.273, S.274, Y.290 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:F.20, A:F.187, A:A.213, A:F.257, A:F.257, A:Y.290 Hydrogen bonds: A:F.20, A:N.22, A:N.22, A:Y.117, A:Y.189, A:V.252, A:V.252, A:Q.254, A:E.272, A:E.272, A:D.273, A:S.274 Water bridges: A:G.24, A:G.24, A:G.24, A:Y.117, A:R.270 Salt bridges: A:R.270 TRH.5: 21 residues within 4Å: Chain B: I.17, D.18, F.20, G.21, N.22, L.54, Y.117, F.187, Y.189, A.213, F.251, V.252, P.253, Q.254, F.257, R.270, G.271, E.272, D.273, S.274, Y.290 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:I.17, B:F.187, B:A.213, B:F.251, B:F.257, B:Y.290 Hydrogen bonds: B:N.22, B:Y.117, B:Y.189, B:V.252, B:V.252, B:Q.254, B:E.272, B:E.272, B:D.273, B:S.274 Water bridges: B:D.18, B:F.20, B:G.21, B:R.270 Salt bridges: B:R.270 pi-Stacking: B:F.251

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

SO4.2: 4 residues within 4Å: Chain A: H.348, Q.349, N.350, G.351 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.350, A:N.350, A:G.351 Water bridges: A:E.315, A:H.348 Salt bridges: A:H.348 SO4.3: 3 residues within 4Å: Chain A: R.202, T.241, A.242 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.241, A:A.242 Water bridges: A:T.241 Salt bridges: A:R.202 SO4.4: 5 residues within 4Å: Chain A: F.187, G.214, T.215, Q.216, R.270 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.215, A:Q.216, A:Q.216 Water bridges: A:I.217, A:R.270, A:R.270 Salt bridges: A:R.270 SO4.6: 7 residues within 4Å: Chain B: F.20, F.187, G.188, G.214, T.215, Q.216, R.270 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.215, B:Q.216, B:Q.216 Water bridges: B:I.217 Salt bridges: B:R.270 SO4.7: 4 residues within 4Å: Chain B: H.348, Q.349, N.350, G.351 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.350, B:N.350, B:G.351 Water bridges: B:H.348, B:Q.349 Salt bridges: B:H.348

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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