SMTL ID : 2xdv.2 (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-dimer

Ligands

2 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:L.153, 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 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:L.153, 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

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

NI.2: 4 residues within 4Å: Chain A: H.156, D.158, H.217 Ligands: OGA.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.156, A:D.158, A:H.217, H2O.6 NI.3: 2 residues within 4Å: Chain A: H.172, D.220 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.172, A:D.220, A:D.220, H2O.4 NI.4: 1 residues within 4Å: Chain A: H.314 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.314, H2O.5 NI.5: 2 residues within 4Å: Chain A: H.400, E.425 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.400 NI.6: 2 residues within 4Å: Chain A: D.106, H.115 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.106, A:D.106, A:H.115, H2O.1 NI.7: 2 residues within 4Å: Chain A: H.392, E.436 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.392, A:E.436, A:E.436, H2O.6 NI.15: 4 residues within 4Å: Chain B: H.156, D.158, H.217 Ligands: OGA.14 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.156, B:D.158, B:H.217, H2O.12 NI.16: 2 residues within 4Å: Chain B: H.172, D.220 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.172, B:D.220, B:D.220, H2O.9 NI.17: 1 residues within 4Å: Chain B: H.314 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.314, H2O.11 NI.18: 2 residues within 4Å: Chain B: H.400, E.425 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.400 NI.19: 2 residues within 4Å: Chain B: D.106, H.115 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.106, B:D.106, B:H.115, H2O.7 NI.20: 2 residues within 4Å: Chain B: H.392, E.436 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.392, B:E.436, B:E.436, H2O.12

2 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

4 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

6 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.11: 3 residues within 4Å: Chain A: C.133, D.347, H.348 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.133, A:D.347, A:H.348, H2O.3, H2O.6 CD.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CD.13: 1 residues within 4Å: Chain A: C.437 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.437 CD.24: 3 residues within 4Å: Chain B: C.133, D.347, H.348 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.133, B:D.347, B:H.348, H2O.8, H2O.11 CD.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CD.26: 1 residues within 4Å: Chain B: C.437 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.437

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

MYC-INDUCED NUCLEAR ANTIGEN

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