SMTL ID : 6d66.1

Crystal structure of the human dual specificity 1 catalytic domain (C258S) as a maltose binding protein fusion in complex with the designed AR protein mbp3_16

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

hetero-1-1-mer

Ligands

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

PEG.1: 5 residues within 4Å: Chain A: E.154, F.157, W.231 Ligands: EDO.7, EDO.19 No protein-ligand interaction detected (PLIP) PEG.17: 3 residues within 4Å: Chain A: K.278, E.279, E.282 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.81, A:A.83, A:K.278 PEG.22: 4 residues within 4Å: Chain B: E.64, E.97, V.98, K.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.64, B:E.97, B:K.101

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: D.427, S.458, Q.459, A.460, G.461, I.462, S.463, R.464 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.458, A:S.458, A:S.458, A:Q.459, A:A.460, A:G.461, A:I.462, A:S.463, A:R.464 Water bridges: A:R.464 Salt bridges: A:R.464

3 x GLY: GLYCINE(Non-covalent)

GLY.3: 3 residues within 4Å: Chain A: A.325, Q.326, I.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.326 Water bridges: A:I.330 GLY.12: 2 residues within 4Å: Chain A: D.482, M.502 No protein-ligand interaction detected (PLIP) GLY.13: 3 residues within 4Å: Chain A: S.435, W.436, E.439 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:S.435, A:S.435, G.13, G.13

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

PGE.4: 4 residues within 4Å: Chain A: Y.91, F.93, M.322, Q.326 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: G.3, A:Q.326 PGE.11: 1 residues within 4Å: Chain A: K.128 No protein-ligand interaction detected (PLIP) PGE.15: 7 residues within 4Å: Chain A: E.23, K.27, N.283, Y.284, T.287, E.289, G.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.23, A:E.23

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

EDO.5: 3 residues within 4Å: Chain A: K.430, D.432, Q.504 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.429 EDO.6: 2 residues within 4Å: Chain A: Q.419, S.446 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.419 EDO.7: 3 residues within 4Å: Chain A: D.66, M.331 Ligands: PEG.1 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain A: N.350, R.355, A.397, R.453 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.453 EDO.10: 3 residues within 4Å: Chain A: S.496, P.497, F.499 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.497 EDO.14: 4 residues within 4Å: Chain A: D.96, Y.172, Y.177, I.330 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.177 EDO.16: 2 residues within 4Å: Chain A: E.292, Y.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.292, A:Y.308 EDO.18: 1 residues within 4Å: Chain A: D.427 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.427 EDO.19: 2 residues within 4Å: Chain A: Y.211 Ligands: PEG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.231 EDO.20: 1 residues within 4Å: Chain B: D.122 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.122 EDO.21: 4 residues within 4Å: Chain A: K.141, A.142 Chain B: H.23, W.57 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.141, B:H.23 EDO.24: 4 residues within 4Å: Chain B: Q.26, D.27, D.28, E.29 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.27, B:D.28, B:E.29

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 2 residues within 4Å: Chain A: A.84, Q.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.87

1 x DAL: D-ALANINE(Non-covalent)

DAL.23: 2 residues within 4Å: Chain B: R.31, Y.69 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.69 Salt bridges: B:R.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gumpena, R. et al., MBP-binding DARPins facilitate the crystallization of an MBP fusion protein. Acta Crystallogr F Struct Biol Commun (2018)

Release Date

2018-09-19

Peptides

Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1: A
Designed AR protein mbp3_16: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1

Designed AR protein mbp3_16

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