SMTL ID : 5wxj.1

Apo EarP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

BME.1: 7 residues within 4Å: Chain A: W.25, L.52, C.53, H.63, Q.64, Q.252, Q.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.64, A:Q.253 BME.2: 3 residues within 4Å: Chain A: Y.157, C.158, R.359 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.359 BME.10: 8 residues within 4Å: Chain B: W.25, R.29, L.52, C.53, H.63, Q.64, Q.252, Q.253 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.29, B:Q.252, B:Q.252, B:Q.253 BME.11: 2 residues within 4Å: Chain B: C.158, F.362 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.358, B:S.358

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

SO4.3: 4 residues within 4Å: Chain A: G.212, T.213, Q.214, R.268 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.213, A:Q.214, A:Q.214 Water bridges: A:I.215, A:R.268, A:R.268 Salt bridges: A:R.268 SO4.4: 4 residues within 4Å: Chain A: H.346, Q.347, N.348, G.349 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: 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 SO4.5: 4 residues within 4Å: Chain A: D.20, F.185, Y.187, R.268 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.187, A:Y.187 Water bridges: A:D.271 Salt bridges: A:R.268 SO4.6: 5 residues within 4Å: Chain A: V.46, R.50, P.57, D.58, V.59 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.57, 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:T.239, A:A.240 SO4.9: 1 residues within 4Å: Chain B: Q.64 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.64 SO4.12: 4 residues within 4Å: Chain B: G.212, T.213, Q.214, R.268 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.213, B:Q.214, B:Q.214 Water bridges: B:I.215, B:R.268 Salt bridges: B:R.268 SO4.13: 4 residues within 4Å: Chain B: H.346, Q.347, N.348, G.349 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.348, B:N.348, B:G.349 Water bridges: B:Q.345, B:H.346, B:H.346 Salt bridges: B:H.346 SO4.14: 4 residues within 4Å: Chain B: D.20, F.185, Y.187, R.268 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.20, B:Y.187 Water bridges: B:D.271 Salt bridges: B:R.268 SO4.15: 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

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: P.60, C.61, V.62, R.69, T.80 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.61, A:T.80 GOL.16: 6 residues within 4Å: Chain B: S.180, W.182, C.264, Q.344, Q.347, W.350 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.180, B:S.180, B:Q.344 Water bridges: B:Q.347, B:Q.347

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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