SMTL ID : 3o9p.2 (1 other biounit)

The structure of the Escherichia coli murein tripeptide binding protein MppA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-hexamer

Ligands

6 x MHI: L-ALA-GAMMA-D-GLU-MESO-DIAMINOPIMELIC ACID(Non-covalent)

MHI.1: 18 residues within 4Å: Chain A: K.24, V.36, G.37, L.38, P.39, I.41, F.113, S.249, Q.271, R.406, R.415, S.417, W.418, V.419, D.421, Y.487, T.488, N.489 35 PLIP interactions: 35 interactions with chain A Hydrophobic interactions: A:L.38, A:I.41, A:V.419, A:V.419, A:Y.487 Hydrogen bonds: A:V.36, A:L.38, A:Q.271, A:S.417, A:S.417, A:S.417, A:S.417, A:V.419, A:D.421, A:T.488 Water bridges: A:S.249, A:S.249, A:S.249, A:K.252, A:K.252, A:K.252, A:Q.271, A:E.313, A:Y.402, A:R.415, A:R.415, A:R.415, A:R.415, A:Y.487, A:Y.487 Salt bridges: A:K.24, A:K.24, A:H.373, A:R.406, A:R.415 MHI.6: 18 residues within 4Å: Chain B: K.24, V.36, G.37, L.38, P.39, I.41, F.113, S.249, Q.271, R.406, R.415, S.417, W.418, V.419, D.421, Y.487, T.488, N.489 35 PLIP interactions: 35 interactions with chain B Hydrophobic interactions: B:L.38, B:I.41, B:V.419, B:V.419, B:Y.487 Hydrogen bonds: B:V.36, B:L.38, B:Q.271, B:S.417, B:S.417, B:S.417, B:S.417, B:V.419, B:D.421, B:T.488 Water bridges: B:S.249, B:S.249, B:S.249, B:K.252, B:K.252, B:K.252, B:Q.271, B:E.313, B:Y.402, B:R.415, B:R.415, B:R.415, B:R.415, B:Y.487, B:Y.487 Salt bridges: B:K.24, B:K.24, B:H.373, B:R.406, B:R.415 MHI.11: 18 residues within 4Å: Chain C: K.24, V.36, G.37, L.38, P.39, I.41, F.113, S.249, Q.271, R.406, R.415, S.417, W.418, V.419, D.421, Y.487, T.488, N.489 35 PLIP interactions: 35 interactions with chain C Hydrophobic interactions: C:L.38, C:I.41, C:V.419, C:V.419, C:Y.487 Hydrogen bonds: C:V.36, C:L.38, C:Q.271, C:S.417, C:S.417, C:S.417, C:S.417, C:V.419, C:D.421, C:T.488 Water bridges: C:S.249, C:S.249, C:S.249, C:K.252, C:K.252, C:K.252, C:Q.271, C:E.313, C:Y.402, C:R.415, C:R.415, C:R.415, C:R.415, C:Y.487, C:Y.487 Salt bridges: C:K.24, C:K.24, C:H.373, C:R.406, C:R.415 MHI.16: 18 residues within 4Å: Chain D: K.24, V.36, G.37, L.38, P.39, I.41, F.113, S.249, Q.271, R.406, R.415, S.417, W.418, V.419, D.421, Y.487, T.488, N.489 35 PLIP interactions: 35 interactions with chain D Hydrophobic interactions: D:L.38, D:I.41, D:V.419, D:V.419, D:Y.487 Hydrogen bonds: D:V.36, D:L.38, D:Q.271, D:S.417, D:S.417, D:S.417, D:S.417, D:V.419, D:D.421, D:T.488 Water bridges: D:S.249, D:S.249, D:S.249, D:K.252, D:K.252, D:K.252, D:Q.271, D:E.313, D:Y.402, D:R.415, D:R.415, D:R.415, D:R.415, D:Y.487, D:Y.487 Salt bridges: D:K.24, D:K.24, D:H.373, D:R.406, D:R.415 MHI.21: 18 residues within 4Å: Chain E: K.24, V.36, G.37, L.38, P.39, I.41, F.113, S.249, Q.271, R.406, R.415, S.417, W.418, V.419, D.421, Y.487, T.488, N.489 35 PLIP interactions: 35 interactions with chain E Hydrophobic interactions: E:L.38, E:I.41, E:V.419, E:V.419, E:Y.487 Hydrogen bonds: E:V.36, E:L.38, E:Q.271, E:S.417, E:S.417, E:S.417, E:S.417, E:V.419, E:D.421, E:T.488 Water bridges: E:S.249, E:S.249, E:S.249, E:K.252, E:K.252, E:K.252, E:Q.271, E:E.313, E:Y.402, E:R.415, E:R.415, E:R.415, E:R.415, E:Y.487, E:Y.487 Salt bridges: E:K.24, E:K.24, E:H.373, E:R.406, E:R.415 MHI.26: 18 residues within 4Å: Chain F: K.24, V.36, G.37, L.38, P.39, I.41, F.113, S.249, Q.271, R.406, R.415, S.417, W.418, V.419, D.421, Y.487, T.488, N.489 35 PLIP interactions: 35 interactions with chain F Hydrophobic interactions: F:L.38, F:I.41, F:V.419, F:V.419, F:Y.487 Hydrogen bonds: F:V.36, F:L.38, F:Q.271, F:S.417, F:S.417, F:S.417, F:S.417, F:V.419, F:D.421, F:T.488 Water bridges: F:S.249, F:S.249, F:S.249, F:K.252, F:K.252, F:K.252, F:Q.271, F:E.313, F:Y.402, F:R.415, F:R.415, F:R.415, F:R.415, F:Y.487, F:Y.487 Salt bridges: F:K.24, F:K.24, F:H.373, F:R.406, F:R.415

24 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: D.82, H.146 Chain E: Q.454, E.458, A.463, D.467 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: E:E.458, E:D.467, E:D.467, A:H.146, H2O.7 ZN.3: 2 residues within 4Å: Chain A: H.212 Chain E: E.477 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: E:E.477, E:E.477, A:H.212, H2O.9 ZN.4: 3 residues within 4Å: Chain A: H.318, D.322, P.329 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.318, A:D.322, H2O.5, H2O.6 ZN.5: 2 residues within 4Å: Chain A: W.496, H.519 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.519, H2O.1, H2O.11, H2O.13 ZN.7: 6 residues within 4Å: Chain B: D.82, H.146 Chain F: Q.454, E.458, A.463, D.467 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: F:E.458, F:D.467, F:D.467, B:H.146, H2O.20 ZN.8: 2 residues within 4Å: Chain B: H.212 Chain F: E.477 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: B:H.212, F:E.477, F:E.477, H2O.22 ZN.9: 3 residues within 4Å: Chain B: H.318, D.322, P.329 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.318, B:D.322, H2O.18, H2O.19 ZN.10: 2 residues within 4Å: Chain B: W.496, H.519 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.519, H2O.14, H2O.24, H2O.26 ZN.12: 6 residues within 4Å: Chain C: D.82, H.146 Chain D: Q.454, E.458, A.463, D.467 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:E.458, D:D.467, D:D.467, C:H.146, H2O.33 ZN.13: 2 residues within 4Å: Chain C: H.212 Chain D: E.477 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:H.212, D:E.477, D:E.477, H2O.35 ZN.14: 3 residues within 4Å: Chain C: H.318, D.322, P.329 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.318, C:D.322, H2O.31, H2O.32 ZN.15: 2 residues within 4Å: Chain C: W.496, H.519 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.519, H2O.27, H2O.37, H2O.39 ZN.17: 6 residues within 4Å: Chain B: Q.454, E.458, A.463, D.467 Chain D: D.82, H.146 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:E.458, B:D.467, B:D.467, D:H.146, H2O.46 ZN.18: 2 residues within 4Å: Chain B: E.477 Chain D: H.212 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:H.212, B:E.477, B:E.477, H2O.48 ZN.19: 3 residues within 4Å: Chain D: H.318, D.322, P.329 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.318, D:D.322, H2O.44, H2O.45 ZN.20: 2 residues within 4Å: Chain D: W.496, H.519 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.519, H2O.40, H2O.50, H2O.52 ZN.22: 6 residues within 4Å: Chain C: Q.454, E.458, A.463, D.467 Chain E: D.82, H.146 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: C:E.458, C:D.467, C:D.467, E:H.146, H2O.59 ZN.23: 2 residues within 4Å: Chain C: E.477 Chain E: H.212 4 PLIP interactions: 1 interactions with chain E, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: E:H.212, C:E.477, C:E.477, H2O.61 ZN.24: 3 residues within 4Å: Chain E: H.318, D.322, P.329 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.318, E:D.322, H2O.57, H2O.58 ZN.25: 2 residues within 4Å: Chain E: W.496, H.519 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:H.519, H2O.53, H2O.63, H2O.65 ZN.27: 6 residues within 4Å: Chain A: Q.454, E.458, A.463, D.467 Chain F: D.82, H.146 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: A:E.458, A:D.467, A:D.467, F:H.146, H2O.72 ZN.28: 2 residues within 4Å: Chain A: E.477 Chain F: H.212 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: A:E.477, A:E.477, F:H.212, H2O.74 ZN.29: 3 residues within 4Å: Chain F: H.318, D.322, P.329 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.318, F:D.322, H2O.70, H2O.71 ZN.30: 2 residues within 4Å: Chain F: W.496, H.519 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:H.519, H2O.66, H2O.76, H2O.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maqbool, A. et al., Compensating Stereochemical Changes Allow Murein Tripeptide to Be Accommodated in a Conventional Peptide-binding Protein. J.Biol.Chem. (2011)

Release Date

2011-07-06

Peptides

Periplasmic murein peptide-binding protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Periplasmic murein peptide-binding protein

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