SMTL ID : 4bjp.1

Crystal structure of E. coli penicillin binding protein 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.338, Q.339, R.340 Ligands: CXS.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.339, A:R.340 Water bridges: A:R.340 SO4.2: 1 residues within 4Å: Chain A: R.391 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.391 Salt bridges: A:R.391 SO4.3: 3 residues within 4Å: Chain A: K.321 Chain B: K.321 Ligands: SO4.32 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.321, B:K.321 SO4.4: 2 residues within 4Å: Chain A: R.11, K.382 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.11, A:K.382 SO4.30: 4 residues within 4Å: Chain B: K.338, Q.339, R.340 Ligands: CXS.35 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.339, B:R.340 Water bridges: B:R.340 SO4.31: 1 residues within 4Å: Chain B: R.391 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.391 Salt bridges: B:R.391 SO4.32: 3 residues within 4Å: Chain A: K.321 Chain B: K.321 Ligands: SO4.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.321, B:K.321 SO4.33: 2 residues within 4Å: Chain B: R.11, K.382 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.11, B:K.382

6 x CXS: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID(Non-covalent)

CXS.5: 5 residues within 4Å: Chain A: E.238, M.356, G.439, R.440, Y.441 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.441 CXS.6: 5 residues within 4Å: Chain A: Q.337, Q.339, R.340 Ligands: SO4.1, EDO.21 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.337, A:Q.339 Salt bridges: A:R.340 CXS.7: 4 residues within 4Å: Chain A: R.258, E.259, N.260 Ligands: GOL.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.259 Hydrogen bonds: A:N.260 Water bridges: A:E.259, A:E.259 Salt bridges: A:R.258 CXS.34: 5 residues within 4Å: Chain B: E.238, M.356, G.439, R.440, Y.441 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.441 CXS.35: 5 residues within 4Å: Chain B: Q.337, Q.339, R.340 Ligands: SO4.30, EDO.50 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.337, B:Q.339 Salt bridges: B:R.340 CXS.36: 4 residues within 4Å: Chain B: R.258, E.259, N.260 Ligands: GOL.40 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:E.259 Hydrogen bonds: B:N.260 Water bridges: B:E.259, B:E.259 Salt bridges: B:R.258

22 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: Q.253, R.316, F.393 Ligands: GOL.9 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: R.391, V.392, F.393, P.394 Ligands: GOL.8 Ligand excluded by PLIP GOL.10: 8 residues within 4Å: Chain A: S.193, G.194, S.195, R.231, D.235, I.446, V.465, N.467 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: E.259, T.285, L.286, T.287 Ligands: CXS.7 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: A.185, F.188, N.189, V.483 Ligand excluded by PLIP GOL.13: 1 residues within 4Å: Chain A: R.14 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain A: N.165, L.166, A.167, T.381, K.382 Chain B: D.384, P.385 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain A: R.254, S.308, A.309, D.312 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain A: N.324, L.378, S.379 Chain B: V.387, P.388, G.389 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain A: S.241, V.278, S.293, T.429, G.430, T.431, Y.448 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain A: S.396, R.399, T.400, H.403 Ligand excluded by PLIP GOL.37: 4 residues within 4Å: Chain B: Q.253, R.316, F.393 Ligands: GOL.38 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain B: R.391, V.392, F.393, P.394 Ligands: GOL.37 Ligand excluded by PLIP GOL.39: 8 residues within 4Å: Chain B: S.193, G.194, S.195, R.231, D.235, I.446, V.465, N.467 Ligand excluded by PLIP GOL.40: 5 residues within 4Å: Chain B: E.259, T.285, L.286, T.287 Ligands: CXS.36 Ligand excluded by PLIP GOL.41: 4 residues within 4Å: Chain B: A.185, F.188, N.189, V.483 Ligand excluded by PLIP GOL.42: 1 residues within 4Å: Chain B: R.14 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain A: D.384, P.385 Chain B: N.165, L.166, A.167, T.381, K.382 Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain B: R.254, S.308, A.309, D.312 Ligand excluded by PLIP GOL.45: 6 residues within 4Å: Chain A: V.387, P.388, G.389 Chain B: N.324, L.378, S.379 Ligand excluded by PLIP GOL.46: 7 residues within 4Å: Chain B: S.241, V.278, S.293, T.429, G.430, T.431, Y.448 Ligand excluded by PLIP GOL.47: 4 residues within 4Å: Chain B: S.396, R.399, T.400, H.403 Ligand excluded by PLIP

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

EDO.19: 2 residues within 4Å: Chain A: R.331, M.356 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain A: L.16, Y.103, P.104, S.105, G.106, T.109, A.110, I.113, P.217 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: Q.337, K.338, Q.339 Ligands: CXS.6 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain A: V.328, G.329 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: F.237, E.238, M.356, K.433, K.434, V.435, I.446 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain A: H.164, N.165 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: S.129, F.130, D.131, K.132, W.133 Ligand excluded by PLIP EDO.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: L.303, A.304, M.305, P.306, R.346 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain A: G.255, V.257, R.258 Ligand excluded by PLIP EDO.48: 2 residues within 4Å: Chain B: R.331, M.356 Ligand excluded by PLIP EDO.49: 9 residues within 4Å: Chain B: L.16, Y.103, P.104, S.105, G.106, T.109, A.110, I.113, P.217 Ligand excluded by PLIP EDO.50: 4 residues within 4Å: Chain B: Q.337, K.338, Q.339 Ligands: CXS.35 Ligand excluded by PLIP EDO.51: 2 residues within 4Å: Chain B: V.328, G.329 Ligand excluded by PLIP EDO.52: 7 residues within 4Å: Chain B: F.237, E.238, M.356, K.433, K.434, V.435, I.446 Ligand excluded by PLIP EDO.53: 2 residues within 4Å: Chain B: H.164, N.165 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain B: S.129, F.130, D.131, K.132, W.133 Ligand excluded by PLIP EDO.55: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.56: 5 residues within 4Å: Chain B: L.303, A.304, M.305, P.306, R.346 Ligand excluded by PLIP EDO.57: 3 residues within 4Å: Chain B: G.255, V.257, R.258 Ligand excluded by PLIP

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

CL.29: 3 residues within 4Å: Chain A: E.192, K.434, N.467 Ligand excluded by PLIP CL.58: 3 residues within 4Å: Chain B: E.192, K.434, N.467 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sauvage, E. et al., Crystal Structure of Penicillin-Binding Protein 3 (Pbp3) from Escherichia Coli. Plos One (2014)

Release Date

2014-05-07

Peptides

PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN