SMTL ID : 7cd4.1

Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.6, H.9, E.48 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.6, A:H.9, A:E.48, A:E.48 ZN.7: 1 residues within 4Å: Chain B: E.48 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.48 ZN.11: 3 residues within 4Å: Chain C: H.6, H.9, E.48 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.6, C:H.9, C:E.48

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

CL.2: 3 residues within 4Å: Chain A: H.6, H.51, Q.93 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: K.73, R.102 Chain D: K.73, R.102 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: V.71, V.72, H.98, A.101 Chain D: N.24 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: K.58, Y.94 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: H.51, Q.93 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: N.24 Chain C: V.71, V.72, H.98, A.101 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain C: H.6, H.51, Q.93 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain D: K.47, H.51, Q.93 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain A: N.24 Chain D: V.71, V.72, H.98, P.100, A.101 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain D: K.58, S.67, F.68 Ligand excluded by PLIP

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.6: 11 residues within 4Å: Chain A: G.31, F.77, R.109, L.110, E.117, E.119 Chain C: S.30, G.31, F.77, E.117, E.119 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:G.31, A:R.109, A:E.119, C:G.31, C:G.31, C:E.117 Salt bridges: A:E.117, C:E.117, C:E.119

3 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 1 residues within 4Å: Chain B: D.96 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.96, H2O.4, H2O.4, H2O.4, H2O.4 MG.13: 2 residues within 4Å: Chain A: E.106 Chain C: E.119 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.119, H2O.1, H2O.1, H2O.6, H2O.6, H2O.7 MG.17: 1 residues within 4Å: Chain D: E.119 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:E.119, H2O.4, H2O.5, H2O.7, H2O.8, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujimoto, Z. et al., Tetramer formation of Bacillus subtilis YabJ protein that belongs to YjgF/YER057c/UK114 family. Biosci.Biotechnol.Biochem. (2021)

Release Date

2021-03-03

Peptides

YabJ protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

YabJ protein

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