SMTL ID : 2qaa.1 (2 other biounits)

Crystal structure of the second tetrahedral intermediates of SGPB at pH 7.3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.23 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: T.112, R.131, T.132, N.133, T.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.112, A:T.167 Salt bridges: A:R.131 SO4.2: 4 residues within 4Å: Chain A: R.100, G.105, T.106 Ligands: EDO.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.106 Water bridges: A:T.106, A:T.106 Salt bridges: A:R.100

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

CL.3: 2 residues within 4Å: Chain A: G.23 Ligands: EDO.11 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: Y.8, R.13 Ligands: ACY.14 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: Y.26 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: G.148, T.149 Ligands: ACY.15 Ligand excluded by PLIP

1 x TYR: TYROSINE(Covalent)

TYR.7: 13 residues within 4Å: Chain A: H.33, A.136, E.137, P.138, G.139, D.140, S.141, G.157, G.158, S.159, G.160 Ligands: LEU.8, GOL.13 15 PLIP interactions: 9 interactions with chain A, 6 Ligand-Ligand interactions Hydrophobic interactions: A:A.136, A:P.138, L.8, L.8 Hydrogen bonds: A:G.139, A:S.141, A:S.141, A:G.160, L.8 Water bridges: A:A.136, A:A.136, Y.7, Y.7 Salt bridges: A:H.33 pi-Stacking: Y.7

1 x LEU: LEUCINE(Covalent)

LEU.8: 12 residues within 4Å: Chain A: H.33, E.137, P.138, G.139, D.140, S.141, T.155, S.156, G.157, G.158 Ligands: TYR.7, GOL.13 11 PLIP interactions: 5 interactions with chain A, 6 Ligand-Ligand interactions Hydrophobic interactions: A:T.155, Y.7, Y.7 Hydrogen bonds: A:G.139, A:S.141, A:S.141, Y.7, L.8 Salt bridges: A:H.33 Water bridges: Y.7, Y.7

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

EDO.9: 7 residues within 4Å: Chain A: G.4, D.5, R.100, G.101, S.102, G.105 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.100, A:R.100 EDO.10: 6 residues within 4Å: Chain A: S.9, T.11, G.12, C.14, C.34, W.41 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.9, A:C.34 Water bridges: A:S.10, A:T.11 EDO.11: 5 residues within 4Å: Chain A: R.21, S.183, V.184, Y.185 Ligands: CL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.21, A:S.183

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.12: 2 residues within 4Å: Chain A: T.53, R.68 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.53 Salt bridges: A:R.68

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 7 residues within 4Å: Chain A: H.33, F.59, Y.120, S.156, G.157 Ligands: TYR.7, LEU.8 5 PLIP interactions: 3 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: Y.7, Y.7, L.8, A:S.156 Water bridges: A:D.124

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.14: 5 residues within 4Å: Chain A: Y.8, G.12, R.13, R.47 Ligands: CL.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.8, A:R.13 Hydrogen bonds: A:T.11 Water bridges: A:R.47, A:R.47 Salt bridges: A:R.47 ACY.15: 4 residues within 4Å: Chain A: Q.83, G.148, T.149 Ligands: CL.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.149 Hydrogen bonds: A:Q.83

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Streptogrisin-B

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