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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.23 Å

Oligo State

monomer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: T.112, R.131, T.132, N.133, G.166, T.167 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.112 Water bridges: A:T.112, A:T.112, A:N.133, A:G.166 Salt bridges: A:R.131 SO4.2: 3 residues within 4Å: Chain A: N.119, G.121, G.122 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.119, A:G.122 Water bridges: A:G.121, A:G.123 SO4.3: 4 residues within 4Å: Chain A: R.100, G.105, T.106 Ligands: GOL.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.106, A:T.106 Water bridges: A:R.100 Salt bridges: A:R.100

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

CL.4: 2 residues within 4Å: Chain A: G.12, R.47 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: R.13 Ligand excluded by PLIP CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: T.39, T.40 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: H.107, C.162 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: S.55, I.66 Ligand excluded by PLIP

1 x TYR: TYROSINE(Covalent)

TYR.10: 14 residues within 4Å: Chain A: H.33, A.136, E.137, P.138, G.139, D.140, S.141, S.156, G.157, G.158, S.159, G.160 Ligands: LEU.11, GOL.13 13 PLIP interactions: 10 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:A.136, A:P.138, L.11 Hydrogen bonds: A:H.33, A:G.139, A:S.141, A:S.141, A:S.159, L.11, L.11 Water bridges: A:A.136, A:A.136 Salt bridges: A:H.33

1 x LEU: LEUCINE(Covalent)

LEU.11: 12 residues within 4Å: Chain A: H.33, A.136, E.137, P.138, G.139, D.140, S.141, T.155, S.156, G.157 Ligands: TYR.10, GOL.13 11 PLIP interactions: 7 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:A.136, A:T.155, Y.10 Hydrogen bonds: A:H.33, A:G.139, A:S.141, A:S.141, Y.10, L.11, L.11 Salt bridges: A:H.33

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

EDO.12: 6 residues within 4Å: Chain A: A.96, V.97, T.98, Y.146, S.147, G.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.97, A:T.98, A:G.148 Water bridges: A:G.109

3 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.10, LEU.11 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Ligand interactions Hydrogen bonds: A:S.156, Y.10, Y.10, L.11 Water bridges: L.11, L.11 GOL.14: 4 residues within 4Å: Chain A: N.90, N.115, G.128, P.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.90, A:N.115, A:N.115 GOL.15: 4 residues within 4Å: Chain A: T.104, G.105, T.106 Ligands: SO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.106, A:T.106 Water bridges: A:T.106, A:H.107

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

ACY.16: 2 residues within 4Å: Chain A: R.21, S.183 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.21 Salt bridges: A:R.21

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
B

Streptogrisin-B

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