- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- monomer
- Ligands
- 2 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)
- 1 x GAV: GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE(Non-covalent)
GAV.3: 25 residues within 4Å:- Chain A: I.74, D.95, C.98, N.202, H.203, F.204, E.206, Q.208, H.234, H.329, N.330, P.378, G.379, S.380, M.381, S.385, H.404, G.405, A.406, G.407, Y.451, V.478, K.480
- Ligands: MN.4, MN.5
19 PLIP interactions:19 interactions with chain A- Hydrogen bonds: A:N.202, A:N.202, A:Q.208, A:N.330, A:G.379, A:G.379, A:S.380, A:M.381, A:S.385, A:A.406, A:G.407, A:K.480
- Water bridges: A:D.95, A:D.95
- Salt bridges: A:H.203, A:E.206, A:H.234
- pi-Stacking: A:F.204, A:Y.451
- 2 x MN: MANGANESE (II) ION(Non-covalent)
MN.4: 5 residues within 4Å:- Chain A: C.98, H.234, H.329
- Ligands: GAV.3, MN.5
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:C.98, A:H.234, A:H.329
MN.5: 5 residues within 4Å:- Chain A: D.95, C.98, H.203
- Ligands: GAV.3, MN.4
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:D.95, A:C.98, A:H.203
- 9 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 7 residues within 4Å:- Chain A: D.95, G.199, S.200, H.203, R.238, H.242
- Ligands: SO4.12
10 PLIP interactions:10 interactions with chain A- Hydrogen bonds: A:S.200, A:S.200
- Water bridges: A:Q.194, A:G.236, A:R.238, A:H.242, A:H.242
- Salt bridges: A:H.203, A:R.238, A:H.242
SO4.7: 1 residues within 4Å:- Chain A: R.260
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:R.260
SO4.8: 6 residues within 4Å:- Chain A: G.69, Y.70, I.74, G.93, Y.94, K.351
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Y.70, A:Y.94
- Water bridges: A:D.95, A:N.330
- Salt bridges: A:K.351
SO4.9: 2 residues within 4Å:- Chain A: S.184, Q.185
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.185
- Water bridges: A:S.184
SO4.10: 2 residues within 4Å:- Chain A: K.212, R.472
2 PLIP interactions:2 interactions with chain A- Salt bridges: A:K.212, A:R.472
SO4.11: 2 residues within 4Å:- Chain A: R.366, R.369
2 PLIP interactions:2 interactions with chain A- Salt bridges: A:R.366, A:R.369
SO4.12: 5 residues within 4Å:- Chain A: R.190, Q.194, R.238, G.239
- Ligands: SO4.6
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Q.194
- Water bridges: A:R.190, A:R.190, A:R.238
- Salt bridges: A:R.190
SO4.13: 3 residues within 4Å:- Chain A: G.341, K.342, R.343
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:G.341, A:R.343
- Salt bridges: A:R.343
SO4.14: 3 residues within 4Å:- Chain A: S.439, M.440, R.441
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:M.440, A:R.441
- Salt bridges: A:R.441
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Desai, K.K. et al., Structures of the Noncanonical RNA Ligase RtcB Reveal the Mechanism of Histidine Guanylylation. Biochemistry (2013)
- Release Date
- 2013-04-10
- Peptides
- tRNA-splicing ligase RtcB: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- monomer
- Ligands
- 2 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)
- 1 x GAV: GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE(Non-covalent)
- 2 x MN: MANGANESE (II) ION(Non-covalent)
- 9 x SO4: SULFATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Desai, K.K. et al., Structures of the Noncanonical RNA Ligase RtcB Reveal the Mechanism of Histidine Guanylylation. Biochemistry (2013)
- Release Date
- 2013-04-10
- Peptides
- tRNA-splicing ligase RtcB: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A