SMTL ID : 2qa9.1 (1 other biounit)

Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.18 Å

Oligo State

homo-dimer

Ligands

2 x ASP- ALA- ILE- TYR: 4-mer peptide DAIY(Non-covalent)

ASP-ALA-ILE-TYR.1: 17 residues within 4Å: Chain A: H.33, V.118, N.119, Y.120, A.136, E.137, P.138, G.139, D.140, S.141, S.156, G.157, G.158, S.159, G.160, F.169 Ligands: EDO.8 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.118, A:Y.120, A:A.136, A:P.138 Hydrogen bonds: A:G.139, A:S.141, A:S.141, A:S.156, A:G.158, A:G.158, A:G.158, A:G.160 Water bridges: A:A.136 Salt bridges: A:H.33 ASP-ALA-ILE-TYR.11: 17 residues within 4Å: Chain B: H.33, V.118, N.119, Y.120, A.136, E.137, P.138, G.139, D.140, S.141, S.156, G.157, G.158, S.159, G.160, F.169 Ligands: EDO.18 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.118, B:Y.120, B:A.136, B:P.138 Hydrogen bonds: B:G.139, B:S.141, B:S.141, B:S.156, B:G.158, B:G.158, B:G.158, B:G.160 Water bridges: B:A.136 Salt bridges: B:H.33

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

CL.2: 3 residues within 4Å: Chain A: T.112, R.131, T.132 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: R.47 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: T.112, R.131, T.132 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: R.47 Ligand excluded by PLIP

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

SO4.4: 9 residues within 4Å: Chain A: R.100, G.105, T.106 Chain B: R.100, G.105, T.106 Ligands: GOL.10, SO4.14, GOL.20 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.106, A:T.106, B:T.106, B:T.106 Water bridges: A:R.100, A:R.100, B:R.100, B:R.100 Salt bridges: A:R.100, B:R.100 SO4.5: 2 residues within 4Å: Chain A: M.95, R.150 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.92, A:A.96 Salt bridges: A:R.150 SO4.14: 9 residues within 4Å: Chain A: R.100, G.105, T.106 Chain B: R.100, G.105, T.106 Ligands: SO4.4, GOL.10, GOL.20 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.106, A:T.106, B:T.106, B:T.106 Water bridges: A:R.100, A:R.100, B:R.100, B:R.100 Salt bridges: A:R.100, B:R.100 SO4.15: 2 residues within 4Å: Chain B: M.95, R.150 3 PLIP interactions: 3 interactions with chain B Water bridges: B:T.92, B:A.96 Salt bridges: B:R.150

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

EDO.6: 6 residues within 4Å: Chain A: S.9, T.11, G.12, C.14, H.33, C.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.9, A:S.9 Water bridges: A:S.10 EDO.7: 5 residues within 4Å: Chain A: G.12, R.13, P.138, G.139 Chain B: S.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.13, A:P.138 Water bridges: A:T.11 EDO.8: 4 residues within 4Å: Chain A: H.33, D.36, F.59 Ligands: ASP-ALA-ILE-TYR.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.36 EDO.9: 4 residues within 4Å: Chain A: S.10, T.39, T.40, W.42 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.10, A:T.39, A:T.40, A:T.40 Water bridges: A:T.39, A:T.39 EDO.16: 6 residues within 4Å: Chain B: S.9, T.11, G.12, C.14, H.33, C.34 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.9, B:S.9 Water bridges: B:S.10 EDO.17: 5 residues within 4Å: Chain A: S.163 Chain B: G.12, R.13, P.138, G.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.13, B:P.138 Water bridges: B:T.11 EDO.18: 4 residues within 4Å: Chain B: H.33, D.36, F.59 Ligands: ASP-ALA-ILE-TYR.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.36 EDO.19: 4 residues within 4Å: Chain B: S.10, T.39, T.40, W.42 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.10, B:T.39, B:T.40, B:T.40 Water bridges: B:T.39, B:T.39

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 10 residues within 4Å: Chain A: G.4, D.5, R.100, G.101, S.102, G.105 Chain B: T.106, H.107 Ligands: SO4.4, SO4.14 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.5, A:R.100, B:H.107 GOL.20: 10 residues within 4Å: Chain A: T.106, H.107 Chain B: G.4, D.5, R.100, G.101, S.102, G.105 Ligands: SO4.4, SO4.14 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.107, B:D.5, B:R.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, T.W. et al., 1.2A-resolution crystal structures reveal the second tetrahedral intermediates of streptogrisin B (SGPB). Biochim.Biophys.Acta (2008)

Release Date

2007-12-11

Peptides

Streptogrisin-B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
E

Streptogrisin-B

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