SMTL ID : 1wl6.2 (1 other biounit)

Mg-substituted form of E. coli aminopeptidase P

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.271, H.354, T.381, E.383, E.406 Ligands: MG.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.271, A:E.383, A:E.406, H2O.1, H2O.7 MG.2: 7 residues within 4Å: Chain A: Y.229, D.260, D.271, T.273, E.383, E.406 Ligands: MG.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.260, A:D.271, A:E.406, H2O.1, H2O.14 MG.8: 6 residues within 4Å: Chain B: D.271, H.354, T.381, E.383, E.406 Ligands: MG.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.271, B:E.383, B:E.406, H2O.24, H2O.30 MG.9: 7 residues within 4Å: Chain B: Y.229, D.260, D.271, T.273, E.383, E.406 Ligands: MG.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.260, B:D.271, B:E.406, H2O.24, H2O.37

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

CL.3: 4 residues within 4Å: Chain A: R.79, V.80, F.110, S.111 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: H.350, G.351, R.370 Chain B: W.88 Ligands: XPE.5 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: R.79, V.80, F.110, S.111 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: W.88 Chain B: H.350, G.351, R.370 Ligands: XPE.12 Ligand excluded by PLIP

2 x XPE: 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL(Non-covalent)

XPE.5: 10 residues within 4Å: Chain A: Y.229, H.243, H.354, H.361, Y.366, R.370 Chain B: D.38, T.84, W.88 Ligands: CL.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:H.243, A:H.243, A:R.370 Hydrogen bonds: B:D.38 XPE.12: 10 residues within 4Å: Chain A: D.38, T.84, W.88 Chain B: Y.229, H.243, H.354, H.361, Y.366, R.370 Ligands: CL.11 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.370

4 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.6: 4 residues within 4Å: Chain A: H.243, H.350, E.383, R.404 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.383, A:E.383 IPA.7: 5 residues within 4Å: Chain A: R.149, P.159, A.160, T.161, M.162 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.162 Hydrogen bonds: A:R.149 IPA.13: 4 residues within 4Å: Chain B: H.243, H.350, E.383, R.404 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.383, B:E.383 IPA.14: 5 residues within 4Å: Chain B: R.149, P.159, A.160, T.161, M.162 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:M.162 Hydrogen bonds: B:R.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Graham, S.C. et al., Structural and functional implications of metal ion selection in aminopeptidase p, a metalloprotease with a dinuclear metal center. Biochemistry (2005)

Release Date

2005-08-16

Peptides

Xaa-Pro aminopeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Xaa-Pro aminopeptidase

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