SMTL ID : 9cld.1

Crystal structure of maltose binding protein (Apo)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 4 residues within 4Å: Chain A: E.312, A.315, K.316, A.321 No protein-ligand interaction detected (PLIP) PEG.2: 4 residues within 4Å: Chain A: Q.358, E.362, K.365, D.366 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.358, A:E.362, A:D.366 PEG.3: 8 residues within 4Å: Chain A: V.26, K.29, N.285, Y.286, T.289, E.291, G.292, A.295 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.285 PEG.4: 5 residues within 4Å: Chain A: K.4, I.5, E.6, D.58, G.59 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.4, A:D.58 Water bridges: A:G.59, A:G.59, A:G.59 PEG.8: 8 residues within 4Å: Chain A: G.71, G.72, Q.75, Y.102, N.335, I.336, P.337, S.340 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.340 Water bridges: A:G.72, A:G.72 PEG.10: 2 residues within 4Å: Chain A: P.51, Q.52 No protein-ligand interaction detected (PLIP)

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

EDO.5: 3 residues within 4Å: Chain A: D.44, K.45, K.49 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.44, A:D.44, A:K.45, A:K.49 EDO.6: 2 residues within 4Å: Chain A: D.210 Ligands: CD.16 No protein-ligand interaction detected (PLIP) EDO.7: 2 residues within 4Å: Chain A: G.16, D.17 No protein-ligand interaction detected (PLIP) EDO.9: 6 residues within 4Å: Chain A: A.165, A.166, G.168, G.169, Y.170, K.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.165, A:G.168

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.11: 6 residues within 4Å: Chain A: E.156, Y.158, F.159, Y.213, W.233 Ligands: PGE.12 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.347 PGE.12: 6 residues within 4Å: Chain A: N.153, E.156, F.159, Y.213, W.233 Ligands: PGE.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.213 Water bridges: A:N.153, A:Y.213

6 x NA: SODIUM ION(Non-functional Binders)

NA.13: 1 residues within 4Å: Chain A: E.313 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.313 NA.14: 2 residues within 4Å: Chain A: V.38, T.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.38 Water bridges: A:V.40 NA.18: 1 residues within 4Å: Chain A: E.312 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.312 NA.20: 3 residues within 4Å: Chain A: D.187, K.365, Q.368 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.187 NA.21: 3 residues within 4Å: Chain A: P.129, K.130, E.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.130 NA.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x CD: CADMIUM ION(Non-covalent)

CD.15: 2 residues within 4Å: Chain A: D.98, R.101 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.98, A:D.98, H2O.3, H2O.10, H2O.11 CD.16: 2 residues within 4Å: Chain A: D.210 Ligands: EDO.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.210, H2O.5, H2O.10 CD.17: 2 residues within 4Å: Chain A: D.85, A.87 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.85, H2O.10, H2O.11, H2O.11, H2O.12 CD.19: 3 residues within 4Å: Chain A: P.274, N.275, K.276 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:P.274, H2O.9, H2O.9, H2O.9, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qianzhu, H. et al., Rendering Proteins Fluorescent Inconspicuously: Genetically Encoded 4-Cyanotryptophan Conserves Their Structure and Enables the Detection of Ligand Binding Sites. Angew.Chem.Int.Ed.Engl. (2024)

Release Date

2024-12-18

Peptides

Maltose/maltodextrin-binding periplasmic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Maltose/maltodextrin-binding periplasmic protein

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