SMTL ID : 5fai.1

EMG1 N1-Specific Pseudouridine Methyltransferase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 20 residues within 4Å: Chain A: I.75, T.164, S.165, F.166, V.188, G.189, F.191, A.192, V.205, S.206, I.207, S.208, Y.210, P.211, L.212, S.213, A.214, T.217 Ligands: CIT.2, UNX.13 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.75, A:A.214 Hydrogen bonds: A:T.164, A:G.189, A:F.191, A:I.207, A:S.208, A:Y.210, A:L.212, A:A.214, A:T.217 Water bridges: A:R.72, A:R.72, A:A.192, A:A.215 SAH.16: 20 residues within 4Å: Chain B: I.75, T.164, S.165, F.166, V.188, G.189, F.191, A.192, V.205, S.206, I.207, S.208, Y.210, P.211, L.212, S.213, A.214, T.217 Ligands: CIT.17, UNX.28 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.75, B:A.214 Hydrogen bonds: B:T.164, B:T.164, B:G.189, B:F.191, B:I.207, B:S.208, B:Y.210, B:L.212, B:A.214 Water bridges: B:R.72, B:R.72, B:A.192, B:A.215

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 7 residues within 4Å: Chain A: S.165, F.166, S.167, G.194, K.195, P.211 Ligands: SAH.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.166 Hydrogen bonds: A:F.166, A:S.167 Water bridges: A:G.194, A:G.194 CIT.3: 7 residues within 4Å: Chain A: R.113, P.115, R.116, T.117, R.120 Chain B: C.54, R.72 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.116, A:T.117, A:T.117, A:T.117, A:R.120 Water bridges: A:R.113, B:R.72 Salt bridges: A:R.113, A:R.113, A:R.120, A:R.120, B:R.72 CIT.17: 7 residues within 4Å: Chain B: S.165, F.166, S.167, G.194, K.195, P.211 Ligands: SAH.16 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.166 Hydrogen bonds: B:F.166, B:S.167 Water bridges: B:G.194, B:G.194 CIT.18: 7 residues within 4Å: Chain A: C.54, R.72 Chain B: R.113, P.115, R.116, T.117, R.120 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.116, B:T.117, B:T.117, B:T.117, B:R.120 Water bridges: B:R.113, A:R.72 Salt bridges: B:R.113, B:R.113, B:R.120, B:R.120, A:R.72

24 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.4: 5 residues within 4Å: Chain A: N.53, R.72, P.73, D.74, F.118 Ligand excluded by PLIP UNX.5: 3 residues within 4Å: Chain A: P.140, Q.141, K.142 Ligand excluded by PLIP UNX.6: 2 residues within 4Å: Chain A: D.173, R.175 Ligand excluded by PLIP UNX.7: 3 residues within 4Å: Chain A: Y.97, E.107, H.154 Ligand excluded by PLIP UNX.8: 2 residues within 4Å: Chain A: I.26, L.93 Ligand excluded by PLIP UNX.9: 2 residues within 4Å: Chain A: H.99, N.103 Ligand excluded by PLIP UNX.10: 5 residues within 4Å: Chain A: S.39, E.41, R.66, A.71, Q.101 Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain A: R.66, D.67 Ligand excluded by PLIP UNX.12: 2 residues within 4Å: Chain A: E.41, K.102 Ligand excluded by PLIP UNX.13: 3 residues within 4Å: Chain A: R.72 Chain B: R.116 Ligands: SAH.1 Ligand excluded by PLIP UNX.14: 4 residues within 4Å: Chain A: P.211, L.212, S.213 Chain B: D.85 Ligand excluded by PLIP UNX.15: 2 residues within 4Å: Chain A: V.231, I.232 Ligand excluded by PLIP UNX.19: 5 residues within 4Å: Chain B: N.53, R.72, P.73, D.74, F.118 Ligand excluded by PLIP UNX.20: 3 residues within 4Å: Chain B: P.140, Q.141, K.142 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain B: D.173, R.175 Ligand excluded by PLIP UNX.22: 3 residues within 4Å: Chain B: Y.97, E.107, H.154 Ligand excluded by PLIP UNX.23: 2 residues within 4Å: Chain B: I.26, L.93 Ligand excluded by PLIP UNX.24: 2 residues within 4Å: Chain B: H.99, N.103 Ligand excluded by PLIP UNX.25: 5 residues within 4Å: Chain B: S.39, E.41, R.66, A.71, Q.101 Ligand excluded by PLIP UNX.26: 2 residues within 4Å: Chain B: R.66, D.67 Ligand excluded by PLIP UNX.27: 2 residues within 4Å: Chain B: E.41, K.102 Ligand excluded by PLIP UNX.28: 3 residues within 4Å: Chain A: R.116 Chain B: R.72 Ligands: SAH.16 Ligand excluded by PLIP UNX.29: 4 residues within 4Å: Chain A: D.85 Chain B: P.211, L.212, S.213 Ligand excluded by PLIP UNX.30: 2 residues within 4Å: Chain B: V.231, I.232 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

ZENG, H. et al., EMG1 N1-Specific Pseudouridine Methyltransferase. to be published

Release Date

2016-01-20

Peptides

Ribosomal RNA small subunit methyltransferase NEP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ribosomal RNA small subunit methyltransferase NEP1