SMTL ID : 3sey.2 (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 Ligands: GOL.14 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.63, A:R.67, A:R.67, A:E.154, A:Y.156, A:R.345 Water bridges: A:E.45, A:D.66 GLC-GLC.2: 13 residues within 4Å: Chain B: N.13, D.15, K.16, W.63, A.64, D.66, E.112, E.154, P.155, Y.156, F.157, W.341, R.345 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.63, B:Y.156, B:R.345

13 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.4: 2 residues within 4Å: Chain A: P.134, H.204 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.204 ZN.5: 4 residues within 4Å: Chain A: E.173, D.178 Chain B: D.165, Q.254 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.173, A:E.173, A:D.178, B:D.165, H2O.7 ZN.6: 1 residues within 4Å: Chain A: D.83 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.83, H2O.2, H2O.7 ZN.7: 1 residues within 4Å: Chain A: H.40 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.40, A:H.40 ZN.8: 1 residues within 4Å: Chain A: H.220 No protein-ligand interaction detected (PLIP) ZN.9: 2 residues within 4Å: Chain A: E.329 Ligands: ACT.15 2 PLIP interactions: 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.2, ACT.15 ZN.16: 3 residues within 4Å: Chain A: D.165 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.8, H2O.10 ZN.17: 1 residues within 4Å: Chain B: E.39 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.39, B:E.39, H2O.8 ZN.18: 1 residues within 4Å: Chain B: D.56 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.56, B:D.56, H2O.9, H2O.9, H2O.10 ZN.19: 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.10, H2O.10 ZN.20: 2 residues within 4Å: Chain B: E.289, E.292 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.289, B:E.289, B:E.292, B:E.292 ZN.21: 4 residues within 4Å: Chain B: Q.326, G.328, E.329 Ligands: ACT.22 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: ACT.22

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

ACT.10: 4 residues within 4Å: Chain A: E.279, N.283, Y.284 Ligands: ACT.11 No protein-ligand interaction detected (PLIP) ACT.11: 2 residues within 4Å: Chain A: E.279 Ligands: ACT.10 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.283 ACT.12: 5 residues within 4Å: Chain A: V.9, W.11, E.39, G.57, P.58 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.9, A:W.11 Hydrogen bonds: A:W.11 ACT.15: 3 residues within 4Å: Chain A: K.257, E.329 Ligands: ZN.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.257 ACT.22: 2 residues within 4Å: Chain B: E.329 Ligands: ZN.21 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.257

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 5 residues within 4Å: Chain A: N.151, Q.153, E.154, D.210, Y.211 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.151, A:N.151, A:Y.211 Water bridges: A:S.212 GOL.14: 6 residues within 4Å: Chain A: N.13, D.15, K.43, E.45, W.63 Ligands: GLC-GLC.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.13, A:K.43 Water bridges: A:D.42, A:L.44, A:E.45

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
C

B
E

Maltose-binding periplasmic protein

Related Entries With Identical Sequence