SMTL ID : 2xdv.1 (1 other biounit)

Crystal Structure of the Catalytic Domain of FLJ14393

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

homo-hexamer

Ligands

6 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.1: 11 residues within 4Å: Chain A: Y.144, G.152, L.153, H.156, D.158, K.171, W.173, H.217, H.230, T.232 Ligands: NI.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:L.153, A:H.156, A:H.230 Water bridges: A:L.153, A:A.219 Salt bridges: A:K.171, A:H.217, A:H.230, A:H.230 OGA.14: 11 residues within 4Å: Chain B: Y.144, G.152, L.153, H.156, D.158, K.171, W.173, H.217, H.230, T.232 Ligands: NI.15 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:L.153, B:H.156, B:H.230, B:T.232 Water bridges: B:Y.144, B:Y.144, B:L.153, B:A.219 Salt bridges: B:K.171, B:H.217, B:H.230, B:H.230 OGA.27: 11 residues within 4Å: Chain C: Y.144, G.152, L.153, H.156, D.158, K.171, W.173, H.217, H.230, T.232 Ligands: NI.28 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:L.153, C:H.156, C:H.230, C:T.232 Water bridges: C:L.153, C:A.219 Salt bridges: C:K.171, C:H.217, C:H.230, C:H.230 OGA.40: 11 residues within 4Å: Chain D: Y.144, G.152, L.153, H.156, D.158, K.171, W.173, H.217, H.230, T.232 Ligands: NI.41 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:L.153, D:H.156, D:H.230 Water bridges: D:Y.144, D:Y.144, D:L.153, D:A.219 Salt bridges: D:K.171, D:H.217, D:H.230, D:H.230 OGA.53: 11 residues within 4Å: Chain E: Y.144, G.152, L.153, H.156, D.158, K.171, W.173, H.217, H.230, T.232 Ligands: NI.54 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:L.153, E:H.156, E:H.230 Water bridges: E:L.153, E:A.219 Salt bridges: E:K.171, E:H.217, E:H.230, E:H.230 OGA.66: 11 residues within 4Å: Chain F: Y.144, G.152, L.153, H.156, D.158, K.171, W.173, H.217, H.230, T.232 Ligands: NI.67 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:L.153, F:H.156, F:H.230, F:T.232 Water bridges: F:Y.144, F:Y.144, F:L.153, F:A.219 Salt bridges: F:K.171, F:H.217, F:H.230, F:H.230

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

NI.2: 4 residues within 4Å: Chain A: H.156, D.158, H.217 Ligands: OGA.1 Ligand excluded by PLIP NI.3: 2 residues within 4Å: Chain A: H.172, D.220 Ligand excluded by PLIP NI.4: 1 residues within 4Å: Chain A: H.314 Ligand excluded by PLIP NI.5: 2 residues within 4Å: Chain A: H.400, E.425 Ligand excluded by PLIP NI.6: 2 residues within 4Å: Chain A: D.106, H.115 Ligand excluded by PLIP NI.7: 2 residues within 4Å: Chain A: H.392, E.436 Ligand excluded by PLIP NI.15: 4 residues within 4Å: Chain B: H.156, D.158, H.217 Ligands: OGA.14 Ligand excluded by PLIP NI.16: 2 residues within 4Å: Chain B: H.172, D.220 Ligand excluded by PLIP NI.17: 1 residues within 4Å: Chain B: H.314 Ligand excluded by PLIP NI.18: 2 residues within 4Å: Chain B: H.400, E.425 Ligand excluded by PLIP NI.19: 2 residues within 4Å: Chain B: D.106, H.115 Ligand excluded by PLIP NI.20: 2 residues within 4Å: Chain B: H.392, E.436 Ligand excluded by PLIP NI.28: 4 residues within 4Å: Chain C: H.156, D.158, H.217 Ligands: OGA.27 Ligand excluded by PLIP NI.29: 2 residues within 4Å: Chain C: H.172, D.220 Ligand excluded by PLIP NI.30: 1 residues within 4Å: Chain C: H.314 Ligand excluded by PLIP NI.31: 2 residues within 4Å: Chain C: H.400, E.425 Ligand excluded by PLIP NI.32: 2 residues within 4Å: Chain C: D.106, H.115 Ligand excluded by PLIP NI.33: 2 residues within 4Å: Chain C: H.392, E.436 Ligand excluded by PLIP NI.41: 4 residues within 4Å: Chain D: H.156, D.158, H.217 Ligands: OGA.40 Ligand excluded by PLIP NI.42: 2 residues within 4Å: Chain D: H.172, D.220 Ligand excluded by PLIP NI.43: 1 residues within 4Å: Chain D: H.314 Ligand excluded by PLIP NI.44: 2 residues within 4Å: Chain D: H.400, E.425 Ligand excluded by PLIP NI.45: 2 residues within 4Å: Chain D: D.106, H.115 Ligand excluded by PLIP NI.46: 2 residues within 4Å: Chain D: H.392, E.436 Ligand excluded by PLIP NI.54: 4 residues within 4Å: Chain E: H.156, D.158, H.217 Ligands: OGA.53 Ligand excluded by PLIP NI.55: 2 residues within 4Å: Chain E: H.172, D.220 Ligand excluded by PLIP NI.56: 1 residues within 4Å: Chain E: H.314 Ligand excluded by PLIP NI.57: 2 residues within 4Å: Chain E: H.400, E.425 Ligand excluded by PLIP NI.58: 2 residues within 4Å: Chain E: D.106, H.115 Ligand excluded by PLIP NI.59: 2 residues within 4Å: Chain E: H.392, E.436 Ligand excluded by PLIP NI.67: 4 residues within 4Å: Chain F: H.156, D.158, H.217 Ligands: OGA.66 Ligand excluded by PLIP NI.68: 2 residues within 4Å: Chain F: H.172, D.220 Ligand excluded by PLIP NI.69: 1 residues within 4Å: Chain F: H.314 Ligand excluded by PLIP NI.70: 2 residues within 4Å: Chain F: H.400, E.425 Ligand excluded by PLIP NI.71: 2 residues within 4Å: Chain F: D.106, H.115 Ligand excluded by PLIP NI.72: 2 residues within 4Å: Chain F: H.392, E.436 Ligand excluded by PLIP

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.8: 1 residues within 4Å: Chain A: D.46 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.46 MN.21: 1 residues within 4Å: Chain B: D.46 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.46 MN.34: 1 residues within 4Å: Chain C: D.46 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.46 MN.47: 1 residues within 4Å: Chain D: D.46 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.46 MN.60: 1 residues within 4Å: Chain E: D.46 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.46 MN.73: 1 residues within 4Å: Chain F: D.46 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.46

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

EDO.9: 3 residues within 4Å: Chain A: F.120, K.121, D.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.122 EDO.10: 3 residues within 4Å: Chain A: E.34, Q.38, K.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.39, A:K.39 EDO.22: 3 residues within 4Å: Chain B: F.120, K.121, D.122 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.122 EDO.23: 3 residues within 4Å: Chain B: E.34, Q.38, K.39 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.39, B:K.39 EDO.35: 3 residues within 4Å: Chain C: F.120, K.121, D.122 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.122 EDO.36: 3 residues within 4Å: Chain C: E.34, Q.38, K.39 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.39, C:K.39 EDO.48: 3 residues within 4Å: Chain D: F.120, K.121, D.122 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.122 EDO.49: 3 residues within 4Å: Chain D: E.34, Q.38, K.39 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.39, D:K.39 EDO.61: 3 residues within 4Å: Chain E: F.120, K.121, D.122 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.122 EDO.62: 3 residues within 4Å: Chain E: E.34, Q.38, K.39 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.39, E:K.39 EDO.74: 3 residues within 4Å: Chain F: F.120, K.121, D.122 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.122 EDO.75: 3 residues within 4Å: Chain F: E.34, Q.38, K.39 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.39, F:K.39

18 x CD: CADMIUM ION(Non-covalent)

CD.11: 3 residues within 4Å: Chain A: C.133, D.347, H.348 Ligand excluded by PLIP CD.12: 1 residues within 4Å: Chain E: C.437 Ligand excluded by PLIP CD.13: 2 residues within 4Å: Chain A: C.437 Chain D: C.67 Ligand excluded by PLIP CD.24: 3 residues within 4Å: Chain B: C.133, D.347, H.348 Ligand excluded by PLIP CD.25: 1 residues within 4Å: Chain F: C.437 Ligand excluded by PLIP CD.26: 2 residues within 4Å: Chain B: C.437 Chain C: C.67 Ligand excluded by PLIP CD.37: 3 residues within 4Å: Chain C: C.133, D.347, H.348 Ligand excluded by PLIP CD.38: 1 residues within 4Å: Chain B: C.437 Ligand excluded by PLIP CD.39: 2 residues within 4Å: Chain C: C.437 Chain F: C.67 Ligand excluded by PLIP CD.50: 3 residues within 4Å: Chain D: C.133, D.347, H.348 Ligand excluded by PLIP CD.51: 1 residues within 4Å: Chain A: C.437 Ligand excluded by PLIP CD.52: 2 residues within 4Å: Chain D: C.437 Chain E: C.67 Ligand excluded by PLIP CD.63: 3 residues within 4Å: Chain E: C.133, D.347, H.348 Ligand excluded by PLIP CD.64: 1 residues within 4Å: Chain D: C.437 Ligand excluded by PLIP CD.65: 2 residues within 4Å: Chain A: C.67 Chain E: C.437 Ligand excluded by PLIP CD.76: 3 residues within 4Å: Chain F: C.133, D.347, H.348 Ligand excluded by PLIP CD.77: 1 residues within 4Å: Chain C: C.437 Ligand excluded by PLIP CD.78: 2 residues within 4Å: Chain B: C.67 Chain F: C.437 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chowdhury, R. et al., Ribosomal oxygenases are structurally conserved from prokaryotes to humans. Nature (2014)

Release Date

2010-05-26

Peptides

MYC-INDUCED NUCLEAR ANTIGEN: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

MYC-INDUCED NUCLEAR ANTIGEN

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