SMTL ID : 1o6t.1

Internalin (INLA, Listeria monocytogenes) - functional domain, uncomplexed

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: E.225, D.247 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.247, H2O.5, H2O.15, H2O.16, H2O.16, H2O.16 MG.14: 2 residues within 4Å: Chain B: E.225, D.247 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.247, H2O.32, H2O.42, H2O.43, H2O.43, H2O.43

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 1 residues within 4Å: Chain A: K.271 No protein-ligand interaction detected (PLIP) CA.15: 1 residues within 4Å: Chain B: K.271 No protein-ligand interaction detected (PLIP)

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

CL.3: 1 residues within 4Å: Chain A: N.279 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: K.26, L.51, Q.52 Ligands: SO4.8 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain B: N.279 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: K.26, L.51, Q.52 Ligands: SO4.21 Ligand excluded by PLIP

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

SO4.5: 8 residues within 4Å: Chain A: Y.313, T.315, Y.317, F.337, Y.339 Chain B: T.34 Ligands: MES.10, MES.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.313, B:G.32 Water bridges: A:Y.339 SO4.6: 3 residues within 4Å: Chain A: R.335, N.356, T.378 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.378 Water bridges: A:R.335, A:R.335, A:R.335, A:N.356, A:T.378, A:T.378 Salt bridges: A:R.335 SO4.7: 4 residues within 4Å: Chain A: N.99, F.120 Chain B: R.55, L.56 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:R.55, A:N.121, A:N.121 Hydrogen bonds: A:N.99, A:N.99 SO4.8: 5 residues within 4Å: Chain A: K.26, T.50, L.51, Q.52 Ligands: CL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.52, A:Q.52 Salt bridges: A:K.26 SO4.18: 8 residues within 4Å: Chain A: T.34 Chain B: Y.313, T.315, Y.317, F.337, Y.339 Ligands: MES.23, MES.25 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.317, B:Y.339, A:G.32 Water bridges: B:T.315 SO4.19: 3 residues within 4Å: Chain B: R.335, N.356, T.378 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.378, B:T.378 Water bridges: B:R.335, B:R.335, B:R.335, B:R.335, B:R.335, B:N.356 Salt bridges: B:R.335 SO4.20: 4 residues within 4Å: Chain A: R.55, L.56 Chain B: N.99, F.120 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.99, B:N.99 Water bridges: B:N.121, B:N.121, A:R.55 SO4.21: 5 residues within 4Å: Chain B: K.26, T.50, L.51, Q.52 Ligands: CL.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.50, B:Q.52, B:Q.52 Salt bridges: B:K.26

10 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.9: 3 residues within 4Å: Chain A: N.383, T.454, T.455 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.383, A:T.454, A:T.455 MES.10: 6 residues within 4Å: Chain A: N.291, Y.313, R.335, F.337, W.357 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.313 Water bridges: A:E.293 Salt bridges: A:R.335 MES.11: 4 residues within 4Å: Chain A: E.296, Y.317, F.318 Chain B: K.33 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Water bridges: B:K.33, B:K.33, B:T.34, A:Y.317, A:Y.317 Salt bridges: B:K.33 MES.12: 6 residues within 4Å: Chain A: Y.339, S.359, G.361, H.362, N.383 Ligands: SO4.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.340 Water bridges: A:N.340, A:S.359, A:G.361, A:G.361, A:N.383 Salt bridges: A:H.362 pi-Cation interactions: A:Y.339 MES.13: 4 residues within 4Å: Chain A: D.46, Q.47, T.49, N.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.69 Water bridges: A:K.91 MES.22: 3 residues within 4Å: Chain B: N.383, T.454, T.455 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.383, B:T.454, B:T.454, B:T.455, B:T.455 MES.23: 6 residues within 4Å: Chain B: N.291, Y.313, R.335, F.337, W.357 Ligands: SO4.18 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.313, B:Y.313 Salt bridges: B:R.335 MES.24: 4 residues within 4Å: Chain A: K.33 Chain B: E.296, Y.317, F.318 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.33, A:K.33, A:T.34 Salt bridges: A:K.33 MES.25: 6 residues within 4Å: Chain B: Y.339, S.359, G.361, H.362, N.383 Ligands: SO4.18 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.339, B:N.340 Water bridges: B:N.340, B:S.359, B:G.361, B:G.361, B:N.383 Salt bridges: B:H.362 pi-Cation interactions: B:Y.339 MES.26: 4 residues within 4Å: Chain B: D.46, Q.47, T.49, N.69 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.69 Water bridges: B:K.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schubert, W.-D. et al., Structure of Internalin, a Major Invasion Protein of Listeria Monocytogenes, in Complex with its Human Receptor E-Cadherin. Cell(Cambridge,Mass.) (2002)

Release Date

2002-12-23

Peptides

INTERNALIN A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

INTERNALIN A

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