SMTL ID : 3sey.1 (1 other biounit)

Zn-mediated Polymer of Maltose-binding Protein A216H/K220H by Synthetic Symmetrization (Form II)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 15 residues within 4Å: Chain A: N.13, D.15, K.16, W.63, A.64, D.66, R.67, E.112, E.154, P.155, Y.156, F.157, W.231, W.341, R.345 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.63, A:Y.156, A:R.345 GLC-GLC.18: 15 residues within 4Å: Chain B: N.13, D.15, K.16, W.63, A.64, D.66, R.67, E.112, E.154, P.155, Y.156, F.157, W.231, W.341, R.345 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.63, B:E.154, B:Y.156, B:R.345 Water bridges: B:D.66

20 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.2: 2 residues within 4Å: Chain A: H.216, E.222 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.216, A:E.222, A:E.222 ZN.3: 4 residues within 4Å: Chain A: P.134, H.204 Ligands: ACT.12, ACT.13 4 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions, 2 Ligand-Ligand interactions Metal complexes: A:H.204, H2O.8, ACT.12, ACT.13 ZN.4: 4 residues within 4Å: Chain A: D.165, Q.254 Chain B: E.173, D.178 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.173, B:D.178, A:D.165, H2O.9, H2O.9 ZN.5: 2 residues within 4Å: Chain A: M.1, K.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.2, H2O.6 ZN.6: 1 residues within 4Å: Chain A: H.220 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.220, H2O.9 ZN.7: 1 residues within 4Å: Chain A: H.40 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.40, A:H.40, H2O.5, H2O.7 ZN.8: 1 residues within 4Å: Chain A: D.83 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.83, H2O.7 ZN.9: 2 residues within 4Å: Chain A: G.328, E.329 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.329, H2O.3, H2O.3 ZN.10: 1 residues within 4Å: Chain A: H.220 No protein-ligand interaction detected (PLIP) ZN.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.19: 2 residues within 4Å: Chain B: H.216, E.222 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.216, B:E.222, B:E.222 ZN.20: 4 residues within 4Å: Chain B: P.134, H.204 Ligands: ACT.29, ACT.30 4 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions, 2 Ligand-Ligand interactions Metal complexes: B:H.204, H2O.16, ACT.29, ACT.30 ZN.21: 4 residues within 4Å: Chain A: E.173, D.178 Chain B: D.165, Q.254 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.173, A:D.178, B:D.165, H2O.1, H2O.1 ZN.22: 2 residues within 4Å: Chain B: M.1, K.2 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:K.2, H2O.15 ZN.23: 1 residues within 4Å: Chain B: H.220 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.220, H2O.17 ZN.24: 1 residues within 4Å: Chain B: H.40 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.40, B:H.40, H2O.14, H2O.16 ZN.25: 1 residues within 4Å: Chain B: D.83 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.83, H2O.15 ZN.26: 2 residues within 4Å: Chain B: G.328, E.329 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.329, H2O.11, H2O.11 ZN.27: 1 residues within 4Å: Chain B: H.220 No protein-ligand interaction detected (PLIP) ZN.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 7 residues within 4Å: Chain A: P.134, D.198, L.199, N.202, H.204 Ligands: ZN.3, ACT.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.134 Hydrogen bonds: A:D.198 Salt bridges: A:H.204 ACT.13: 5 residues within 4Å: Chain A: P.134, A.135, H.204 Ligands: ZN.3, ACT.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.134, A:A.135 Salt bridges: A:H.204 ACT.14: 6 residues within 4Å: Chain A: M.1, V.9, W.11, E.39, G.57, P.58 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.11 Hydrogen bonds: A:W.11 ACT.29: 7 residues within 4Å: Chain B: P.134, D.198, L.199, N.202, H.204 Ligands: ZN.20, ACT.30 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.134 Hydrogen bonds: B:D.198 Salt bridges: B:H.204 ACT.30: 5 residues within 4Å: Chain B: P.134, A.135, H.204 Ligands: ZN.20, ACT.29 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.134, B:A.135 Salt bridges: B:H.204 ACT.31: 6 residues within 4Å: Chain B: M.1, V.9, W.11, E.39, G.57, P.58 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.11 Hydrogen bonds: B:W.11

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 7 residues within 4Å: Chain A: Y.91, F.93, V.111, A.302, V.303, E.309, M.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.302 GOL.16: 5 residues within 4Å: Chain A: K.120, Y.243, G.244, V.245, R.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.120, A:V.245, A:V.245 GOL.17: 3 residues within 4Å: Chain A: E.29, K.30, G.33 No protein-ligand interaction detected (PLIP) GOL.32: 7 residues within 4Å: Chain B: Y.91, F.93, V.111, A.302, V.303, E.309, M.322 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.302, B:E.309 GOL.33: 5 residues within 4Å: Chain B: K.120, Y.243, G.244, V.245, R.317 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.120, B:V.245, B:V.245 GOL.34: 3 residues within 4Å: Chain B: E.29, K.30, G.33 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laganowsky, A. et al., An approach to crystallizing proteins by metal-mediated synthetic symmetrization. Protein Sci. (2011)

Release Date

2011-09-21

Peptides

Maltose-binding periplasmic protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Maltose-binding periplasmic protein

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