SMTL ID : 6d65.1 (1 other biounit)

Crystal structure of the human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding protein fusion in complex with the designed AR protein off7

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-1-1-mer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: N.186, A.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.185 Water bridges: A:N.186 GOL.2: 2 residues within 4Å: Chain A: F.195, D.198 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:K.122, B:K.122, A:F.195, A:N.202 Hydrogen bonds: A:D.198 GOL.3: 3 residues within 4Å: Chain A: N.428, H.429, K.430 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.429, A:K.430, A:K.430, A:K.430 GOL.15: 3 residues within 4Å: Chain A: Q.490, R.492, S.493 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.490, A:S.493, A:S.493, A:I.494

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: P.41, D.42, K.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.42 Salt bridges: A:K.47 SO4.5: 3 residues within 4Å: Chain A: R.391, D.393, M.394 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.393, A:M.394 Salt bridges: A:R.391 SO4.6: 3 residues within 4Å: Chain A: Y.420, K.421, S.422 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.422 Water bridges: A:N.412 Salt bridges: A:K.421 SO4.7: 8 residues within 4Å: Chain A: D.427, S.458, Q.459, A.460, G.461, I.462, S.463, R.464 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.458, A:S.458, A:Q.459, A:A.460, A:G.461, A:I.462, A:S.463, A:R.464 Salt bridges: A:R.464 SO4.8: 7 residues within 4Å: Chain A: S.407, A.408, N.409, C.410, E.426, Q.459, R.464 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.408, A:N.409, A:N.409, A:C.410, A:E.426 Water bridges: A:Q.459 Salt bridges: A:R.464 SO4.9: 5 residues within 4Å: Chain A: K.392, F.414, E.415, G.416, H.417 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.415, A:G.416 Salt bridges: A:K.392 SO4.14: 4 residues within 4Å: Chain A: H.429, P.497, N.498, F.499 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.499 Salt bridges: A:H.429 SO4.19: 5 residues within 4Å: Chain A: N.151, Q.153, E.154, D.210, Y.211 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.151, A:E.154, A:E.154, A:Y.211 Water bridges: A:S.212 SO4.20: 4 residues within 4Å: Chain B: G.58, H.59, L.60, E.61 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.60, B:E.61 Water bridges: B:G.58, B:I.62 SO4.21: 4 residues within 4Å: Chain B: G.91, H.92, L.93, E.94 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.93, B:E.94 Water bridges: B:H.92 SO4.22: 4 residues within 4Å: Chain B: G.124, Y.125, L.126, E.127 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.126, B:E.127 Water bridges: B:I.128

9 x EOH: ETHANOL(Non-functional Binders)

EOH.10: 3 residues within 4Å: Chain A: G.14, H.40, D.42 No protein-ligand interaction detected (PLIP) EOH.11: 5 residues within 4Å: Chain A: S.271, P.272, N.273, K.274, E.275 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.274 Hydrogen bonds: A:K.274, A:E.275 EOH.12: 3 residues within 4Å: Chain A: T.287, D.288, E.289 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.288, A:E.289 Hydrogen bonds: A:T.287, A:T.287, A:D.288, A:E.289 EOH.13: 1 residues within 4Å: Chain A: K.314 No protein-ligand interaction detected (PLIP) EOH.16: 1 residues within 4Å: Chain A: R.478 No protein-ligand interaction detected (PLIP) EOH.17: 1 residues within 4Å: Chain A: R.391 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.391, A:R.391 EOH.18: 2 residues within 4Å: Chain A: Y.18, N.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.18 Water bridges: A:Y.18 EOH.23: 3 residues within 4Å: Chain A: K.141 Chain B: R.23, Y.56 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.23, B:Y.56 EOH.24: 3 residues within 4Å: Chain B: N.41, D.72, A.75 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.72, B:A.75 Hydrogen bonds: B:N.41

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 off7: 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 off7

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