SMTL ID : 9clc.1

Crystal structure of maltose binding protein (Apo), mutant Trp10 to 4-Cyanotryptophan

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

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

NA.1: 2 residues within 4Å: Chain A: E.313 Ligands: EDO.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.313 Water bridges: A:E.313 NA.2: 3 residues within 4Å: Chain A: E.31, V.38 Ligands: NA.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.31, A:V.38 NA.9: 3 residues within 4Å: Chain A: E.31, K.37 Ligands: NA.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.31 NA.10: 1 residues within 4Å: Chain A: E.312 No protein-ligand interaction detected (PLIP) NA.22: 3 residues within 4Å: Chain A: P.274, N.275, K.276 3 PLIP interactions: 3 interactions with chain A Water bridges: A:P.274, A:N.275, A:K.276 NA.23: 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

3 x CD: CADMIUM ION(Non-covalent)

CD.3: 2 residues within 4Å: Chain A: D.98, R.101 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.98, A:D.98, H2O.3 CD.4: 2 residues within 4Å: Chain A: D.210 Ligands: EDO.15 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.210 CD.5: 2 residues within 4Å: Chain A: D.85, A.87 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.85, H2O.10

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

PEG.6: 5 residues within 4Å: Chain A: E.312, A.315, K.316, A.321 Ligands: EDO.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.312 PEG.7: 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:D.366, A:D.366 PEG.8: 8 residues within 4Å: Chain A: V.26, K.29, N.285, Y.286, T.289, E.291, G.292, A.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.29, A:N.285 PEG.25: 2 residues within 4Å: Chain A: E.6, K.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.6

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

EDO.11: 5 residues within 4Å: Chain A: K.4, I.5, E.6, D.58, G.59 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.4, A:D.58 Water bridges: A:G.59 EDO.12: 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.14: 6 residues within 4Å: Chain A: D.68, M.333, P.334, M.339, S.340, W.343 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.68, A:M.339, A:W.343 EDO.15: 2 residues within 4Å: Chain A: D.210 Ligands: CD.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.210 EDO.16: 3 residues within 4Å: Chain A: E.291, E.294 Ligands: NA.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.294 EDO.17: 4 residues within 4Å: Chain A: Y.158, F.159, Y.213, W.233 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.153 EDO.18: 3 residues within 4Å: Chain A: T.289, D.290, E.291 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.290, A:D.290 EDO.19: 2 residues within 4Å: Chain A: D.17, K.300 No protein-ligand interaction detected (PLIP) EDO.20: 3 residues within 4Å: Chain A: P.51, Q.52, A.55 No protein-ligand interaction detected (PLIP) EDO.21: 4 residues within 4Å: Chain A: E.312, E.313, K.316 Ligands: PEG.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.316 Water bridges: A:E.313 EDO.24: 5 residues within 4Å: Chain A: A.165, G.168, G.169, Y.170, K.259 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.168, A:G.169, A:K.259

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

PGE.13: 4 residues within 4Å: Chain A: T.196, A.359, V.360, D.361 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.360, A:D.361, A:D.361

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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