SMTL ID : 9jgc.1

Crystal structure of Nep1 in complex with adenosine from Pyrococcus horikoshii OT3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 6 residues within 4Å: Chain A: E.17, T.18, N.95, F.122 Ligands: EDO.8, EDO.9 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain B: E.17, T.18, N.95, F.122 Ligands: EDO.20, EDO.21 Ligand excluded by PLIP

2 x ADN: ADENOSINE(Non-covalent)

ADN.2: 16 residues within 4Å: Chain A: M.156, H.157, E.158, V.182, G.183, F.185, F.190, I.199, S.200, L.201, Y.202, E.204, P.205, L.206, A.208, I.211 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.183, A:L.201, A:Y.202, A:Y.202, A:L.206 Water bridges: A:E.158, A:E.158, A:F.185, A:A.208 ADN.14: 16 residues within 4Å: Chain B: M.156, H.157, E.158, V.182, G.183, F.185, F.190, I.199, S.200, L.201, Y.202, E.204, P.205, L.206, A.208, I.211 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.183, B:L.201, B:Y.202, B:Y.202, B:L.206 Water bridges: B:E.158, B:F.185, B:A.208

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

SO4.3: 3 residues within 4Å: Chain A: K.4, K.5, R.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.5 Water bridges: A:R.86 Salt bridges: A:R.86 SO4.15: 3 residues within 4Å: Chain B: K.4, K.5, R.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.5 Water bridges: B:R.86 Salt bridges: B:R.86

4 x SO3: SULFITE ION(Non-covalent)

SO3.4: 3 residues within 4Å: Chain A: K.38, R.39, K.42 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.38, A:R.39 SO3.5: 5 residues within 4Å: Chain A: R.106, P.108, R.109, N.110, R.113 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.106, A:R.106, A:R.109, A:N.110, A:R.113 SO3.16: 3 residues within 4Å: Chain B: K.38, R.39, K.42 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.38, B:R.39 SO3.17: 5 residues within 4Å: Chain B: R.106, P.108, R.109, N.110, R.113 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.106, B:R.106, B:R.109, B:N.110, B:R.113

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 3 residues within 4Å: Chain A: T.140, N.142, E.143 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.140, A:N.142, A:E.143, A:E.143 Water bridges: A:T.140, A:N.142 EDO.7: 4 residues within 4Å: Chain A: V.89, Y.90, Y.100, I.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.89, A:I.101 Water bridges: A:V.89 EDO.8: 7 residues within 4Å: Chain A: E.17, T.18, P.20, P.21, R.63, N.95 Ligands: CL.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.17, A:T.18, A:T.18, A:R.63, A:N.95 EDO.9: 4 residues within 4Å: Chain A: T.18, Y.97, F.122 Ligands: CL.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.97, A:Y.97, A:F.122 EDO.10: 3 residues within 4Å: Chain A: N.82, D.85, P.103 No protein-ligand interaction detected (PLIP) EDO.11: 5 residues within 4Å: Chain A: H.157, D.189, F.190, K.193, K.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.190, A:K.198, A:K.198 EDO.18: 3 residues within 4Å: Chain B: T.140, N.142, E.143 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.142, B:E.143, B:E.143 Water bridges: B:T.140, B:N.142 EDO.19: 4 residues within 4Å: Chain B: V.89, Y.90, Y.100, I.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.89, B:I.101 Water bridges: B:V.89 EDO.20: 7 residues within 4Å: Chain B: E.17, T.18, P.20, P.21, R.63, N.95 Ligands: CL.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.18, B:R.63, B:N.95 Water bridges: B:T.18 EDO.21: 4 residues within 4Å: Chain B: T.18, Y.97, F.122 Ligands: CL.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.18 Water bridges: B:Y.97, B:F.122 EDO.22: 3 residues within 4Å: Chain B: N.82, D.85, P.103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.85 EDO.23: 5 residues within 4Å: Chain B: H.157, D.189, F.190, K.193, K.198 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.190, B:K.198, B:K.198

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 6 residues within 4Å: Chain A: R.106, R.109 Chain B: R.65, I.68, P.186, M.207 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.106, B:R.65, B:R.65 PEG.24: 6 residues within 4Å: Chain A: R.65, I.68, P.186, M.207 Chain B: R.106, R.109 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.65, A:R.65, B:R.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saha, S. et al., Structural analysis of the ribosome assembly factor Nep1, an N1-specific pseudouridine methyltransferase, reveals mechanistic insights. Febs J. (2025)

Release Date

2025-03-12

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

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