SMTL ID : 5wxk.1

EarP bound with domain I of EF-P

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.1: 18 residues within 4Å: Chain A: N.17, F.18, G.19, G.22, L.52, 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 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.185, A:A.211, A:F.249, A:F.255 Hydrogen bonds: A:F.18, A:G.19, A:Y.187, A:V.250, A:V.250, A:Q.252, A:E.270, A:D.271, A:S.272 Water bridges: A:D.20, B:R.32 Salt bridges: A:R.268 pi-Stacking: A:F.249

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

SO4.2: 6 residues within 4Å: Chain A: F.18, F.185, G.212, T.213, Q.214, R.268 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.213, A:Q.214, A:Q.214 Water bridges: A:I.215, A:R.268 Salt bridges: A:R.268 SO4.3: 4 residues within 4Å: Chain A: S.145, E.146, K.147, Y.360 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.145, A:E.146, A:K.147 Water bridges: A:E.146, A:E.146 SO4.4: 4 residues within 4Å: Chain A: H.32, W.37, Q.38, H.67 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.39, A:H.67 Salt bridges: A:H.32 SO4.5: 4 residues within 4Å: Chain A: V.46, R.50, D.58, V.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.58, A:D.58, A:V.59 Salt bridges: A:R.50

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

BME.6: 5 residues within 4Å: Chain A: A.317, R.320, Q.335, E.338, C.339 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.338 BME.7: 2 residues within 4Å: Chain A: Y.157, C.158 No protein-ligand interaction detected (PLIP) BME.8: 8 residues within 4Å: Chain A: W.25, C.53, P.54, D.55, H.63, Q.64, P.251, Q.253 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.253, A:Q.253, A:D.254

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 2 residues within 4Å: Chain A: G.223, V.224 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.223 GOL.11: 5 residues within 4Å: Chain B: L.7, R.8, A.9, K.24, T.25 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.7, B:A.9, B:T.25, B:T.25

1 x NI: NICKEL (II) ION(Non-covalent)

NI.10: 1 residues within 4Å: Chain A: H.346 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.346

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: A
Elongation factor P: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

EarP

Elongation factor P

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