SMTL ID : 4k1t.1

Gly-Ser-SplB protease from Staphylococcus aureus at 1.60 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

Ligands

20 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.125, E.155 Chain B: D.182 Chain F: G.1 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F, 2 interactions with chain A Metal complexes: B:D.182, F:G.1, A:H.125, A:E.155 ZN.2: 2 residues within 4Å: Chain A: H.41, D.79 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.41, A:D.79, A:D.79, H2O.10, H2O.10 ZN.3: 7 residues within 4Å: Chain A: D.182, D.183 Chain B: D.182, D.183 Chain C: D.182, D.183 Ligands: SO4.4 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Metal complexes: A:D.183, A:D.183, B:D.183, C:D.183, C:D.183 ZN.8: 3 residues within 4Å: Chain A: D.182 Chain C: H.153 Ligands: SO4.9 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:H.153, A:D.182, A:D.182, H2O.1 ZN.10: 3 residues within 4Å: Chain A: H.153 Chain B: D.182 Ligands: SO4.11 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.153, B:D.182, B:D.182, H2O.1 ZN.12: 5 residues within 4Å: Chain B: H.125, E.155 Chain C: D.182, N.184 Chain E: G.1 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain E Metal complexes: B:H.125, B:E.155, C:D.182, E:G.1 ZN.13: 2 residues within 4Å: Chain B: H.41, D.79 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.41, B:D.79, B:D.79, H2O.18, H2O.19 ZN.17: 3 residues within 4Å: Chain B: H.153 Chain C: D.182 Ligands: SO4.18 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:D.182, C:D.182, B:H.153, H2O.10 ZN.19: 5 residues within 4Å: Chain A: D.182, N.184 Chain C: H.125, E.155 Chain D: G.1 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Metal complexes: C:H.125, C:E.155, A:D.182, D:G.1 ZN.20: 2 residues within 4Å: Chain C: H.41, D.79 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.41, C:D.79, H2O.26, H2O.32 ZN.22: 4 residues within 4Å: Chain C: G.1 Chain D: H.125, E.155 Chain E: D.182 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 2 interactions with chain D Metal complexes: C:G.1, E:D.182, D:H.125, D:E.155 ZN.23: 2 residues within 4Å: Chain D: H.41, D.79 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.41, D:D.79, D:D.79, H2O.43, H2O.43 ZN.24: 7 residues within 4Å: Chain D: D.182, D.183 Chain E: D.182, D.183 Chain F: D.182, D.183 Ligands: SO4.25 5 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D, 2 interactions with chain F Metal complexes: E:D.183, D:D.183, D:D.183, F:D.183, F:D.183 ZN.29: 3 residues within 4Å: Chain D: D.182 Chain F: H.153 Ligands: SO4.30 4 PLIP interactions: 1 interactions with chain F, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: F:H.153, D:D.182, D:D.182, H2O.33 ZN.31: 3 residues within 4Å: Chain D: H.153 Chain E: D.182 Ligands: SO4.32 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: D:H.153, E:D.182, E:D.182, H2O.33 ZN.33: 5 residues within 4Å: Chain B: G.1 Chain E: H.125, E.155 Chain F: D.182, N.184 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F, 1 interactions with chain B Metal complexes: E:H.125, E:E.155, F:D.182, B:G.1 ZN.34: 2 residues within 4Å: Chain E: H.41, D.79 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.41, E:D.79, E:D.79, H2O.50, H2O.51 ZN.38: 3 residues within 4Å: Chain E: H.153 Chain F: D.182 Ligands: SO4.39 4 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: E:H.153, F:D.182, F:D.182, H2O.42 ZN.40: 5 residues within 4Å: Chain A: G.1 Chain D: D.182, N.184 Chain F: H.125, E.155 4 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D, 1 interactions with chain A Metal complexes: F:H.125, F:E.155, D:D.182, A:G.1 ZN.41: 2 residues within 4Å: Chain F: H.41, D.79 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.41, F:D.79, H2O.59, H2O.65

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

SO4.4: 10 residues within 4Å: Chain A: D.182, D.183 Chain B: D.182, D.183 Chain C: D.182, D.183 Ligands: ZN.3, SO4.9, SO4.11, SO4.18 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: R.88, N.98 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: K.8, K.10 Chain F: R.117 Ligand excluded by PLIP SO4.9: 8 residues within 4Å: Chain A: D.182 Chain C: N.4, V.6, H.153 Chain D: G.1, S.2 Ligands: SO4.4, ZN.8 Ligand excluded by PLIP SO4.11: 8 residues within 4Å: Chain A: N.4, V.6, H.153 Chain B: D.182 Chain F: G.1, S.2 Ligands: SO4.4, ZN.10 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: K.8, K.10 Chain E: R.117, T.137 Ligand excluded by PLIP SO4.18: 8 residues within 4Å: Chain B: N.4, V.6, H.153 Chain C: D.182 Chain E: G.1, S.2 Ligands: SO4.4, ZN.17 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain C: K.8, K.10 Chain D: R.117, T.137 Ligand excluded by PLIP SO4.25: 10 residues within 4Å: Chain D: D.182, D.183 Chain E: D.182, D.183 Chain F: D.182, D.183 Ligands: ZN.24, SO4.30, SO4.32, SO4.39 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain D: R.88, N.98 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain C: R.117 Chain D: K.8, K.10 Ligand excluded by PLIP SO4.30: 8 residues within 4Å: Chain A: G.1, S.2 Chain D: D.182 Chain F: N.4, V.6, H.153 Ligands: SO4.25, ZN.29 Ligand excluded by PLIP SO4.32: 8 residues within 4Å: Chain C: G.1, S.2 Chain D: N.4, V.6, H.153 Chain E: D.182 Ligands: SO4.25, ZN.31 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain B: R.117, T.137 Chain E: K.8, K.10 Ligand excluded by PLIP SO4.39: 8 residues within 4Å: Chain B: G.1, S.2 Chain E: N.4, V.6, H.153 Chain F: D.182 Ligands: SO4.25, ZN.38 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain A: R.117, T.137 Chain F: K.8, K.10 Ligand excluded by PLIP

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

CL.7: 4 residues within 4Å: Chain A: R.185, N.186 Chain C: S.156, S.177 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: S.156, S.177 Chain B: R.185, N.186 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: S.156, S.177 Chain C: R.185, N.186 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain D: R.185, N.186 Chain F: S.156, S.177 Ligand excluded by PLIP CL.36: 4 residues within 4Å: Chain D: S.156, S.177 Chain E: R.185, N.186 Ligand excluded by PLIP CL.37: 4 residues within 4Å: Chain E: S.156, S.177 Chain F: R.185, N.186 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pustelny, K. et al., Staphylococcal SplB Serine Protease Utilizes a Novel Molecular Mechanism of Activation. J.Biol.Chem. (2014)

Release Date

2014-04-16

Peptides

Serine protease SplB: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Serine protease SplB

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