SMTL ID : 6qkv.1

Structure of YibK from P. aeruginosa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: I.13, N.16, E.104, N.134, L.135 Chain B: N.19, R.22 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.16, A:N.134, A:L.135 Water bridges: A:S.132, A:L.133, A:L.133, B:N.19 Salt bridges: B:R.22 SO4.2: 3 residues within 4Å: Chain A: R.86, V.91, A.92 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:A.92 Water bridges: A:R.76, A:R.86, A:R.86, A:R.86, A:D.119, A:D.119, A:R.120 Salt bridges: A:R.86 SO4.3: 4 residues within 4Å: Chain A: T.81, T.82, K.83, G.107 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.81, A:T.81, A:T.82, A:L.108 SO4.4: 4 residues within 4Å: Chain A: Y.64, Q.66, S.67 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.67 SO4.8: 4 residues within 4Å: Chain B: R.76, R.86, V.91, A.92 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.76, B:A.92 Water bridges: B:R.76, B:R.86, B:R.86, B:A.92, B:R.120 Salt bridges: B:R.86 SO4.9: 4 residues within 4Å: Chain B: T.81, T.82, G.107, L.108 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.82, B:L.108

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain A: R.148, Q.149 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Water bridges: B:R.148, B:R.148, A:H.89, A:H.89, A:Q.149, A:Q.149 Hydrogen bonds: A:R.148, A:R.148 GOL.6: 4 residues within 4Å: Chain A: S.1, H.2, H.5, S.30 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.1, A:H.2, A:H.2, A:H.5, A:S.30 Water bridges: A:H.32 GOL.7: 5 residues within 4Å: Chain A: Y.64, L.65, Q.66, V.112 Ligands: SO4.4 No protein-ligand interaction detected (PLIP) GOL.10: 7 residues within 4Å: Chain B: S.1, H.2, H.5, L.72, P.75, G.96 Ligands: GOL.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.1, B:G.96 GOL.11: 5 residues within 4Å: Chain B: S.1, H.2, H.5, L.72 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.1, B:S.1, B:H.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsu, S.D. et al., Tying up the Loose Ends: A Mathematically Knotted Protein. Front Chem (2021)

Release Date

2020-02-19

Peptides

tRNA (cytidine(34)-2'-O)-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

tRNA (cytidine(34)-2'-O)-methyltransferase