SMTL ID : 5w31.1

Crystal structure of mutant CJ YCEI protein (CJ-N48C) with mercuribenzoic acid guest structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-tetramer

Ligands

4 x UNL: UNKNOWN LIGAND

UNL.1: 12 residues within 4Å: Chain A: F.29, I.52, R.64, L.68, F.74, M.82, L.155, I.159, L.161, I.163 Chain C: F.15, I.17 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.29, A:I.52, A:R.64, A:L.68, A:F.74, A:L.155, A:L.161, A:I.163, C:F.15, C:F.15, C:I.17 UNL.5: 12 residues within 4Å: Chain B: F.29, I.52, R.64, L.68, F.74, M.82, L.155, I.159, L.161, I.163 Chain D: F.15, I.17 11 PLIP interactions: 3 interactions with chain D, 8 interactions with chain B Hydrophobic interactions: D:F.15, D:F.15, D:I.17, B:F.29, B:I.52, B:R.64, B:L.68, B:F.74, B:L.155, B:L.161, B:I.163 UNL.9: 12 residues within 4Å: Chain A: F.15, I.17 Chain C: F.29, I.52, R.64, L.68, F.74, M.82, L.155, I.159, L.161, I.163 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.29, C:I.52, C:R.64, C:L.68, C:F.74, C:L.155, C:L.161, C:I.163, A:F.15, A:F.15, A:I.17 UNL.13: 12 residues within 4Å: Chain B: F.15, I.17 Chain D: F.29, I.52, R.64, L.68, F.74, M.82, L.155, I.159, L.161, I.163 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain D Hydrophobic interactions: B:F.15, B:F.15, B:I.17, D:F.29, D:I.52, D:R.64, D:L.68, D:F.74, D:L.155, D:L.161, D:I.163

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

SO4.2: 3 residues within 4Å: Chain A: S.109, K.110, D.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.109, A:D.111 Salt bridges: A:K.110 SO4.3: 8 residues within 4Å: Chain A: T.150, S.151, T.154 Chain B: S.149, T.150, S.151, T.154 Ligands: SO4.7 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.151, A:T.154, B:S.151, B:T.154 SO4.6: 3 residues within 4Å: Chain B: S.109, K.110, D.111 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.109, B:D.111 Salt bridges: B:K.110 SO4.7: 8 residues within 4Å: Chain A: S.149, T.150, S.151, T.154 Chain B: T.150, S.151, T.154 Ligands: SO4.3 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.151, A:T.154, B:S.151, B:T.154 SO4.10: 3 residues within 4Å: Chain C: S.109, K.110, D.111 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.109, C:D.111 Salt bridges: C:K.110 SO4.11: 8 residues within 4Å: Chain C: T.150, S.151, T.154 Chain D: S.149, T.150, S.151, T.154 Ligands: SO4.15 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.151, D:S.151 SO4.14: 3 residues within 4Å: Chain D: S.109, K.110, D.111 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.109, D:D.111 Salt bridges: D:K.110 SO4.15: 8 residues within 4Å: Chain C: S.149, T.150, S.151, T.154 Chain D: T.150, S.151, T.154 Ligands: SO4.11 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.151, D:S.151

4 x MBO: MERCURIBENZOIC ACID(Non-covalent)

MBO.4: 5 residues within 4Å: Chain A: K.26, G.27, C.28, N.58, E.60 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.26, A:E.60 Metal complexes: A:C.28 MBO.8: 5 residues within 4Å: Chain B: K.26, G.27, C.28, N.58, E.60 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.26, B:E.60 Metal complexes: B:C.28 MBO.12: 5 residues within 4Å: Chain C: K.26, G.27, C.28, N.58, E.60 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.26, C:E.60 Metal complexes: C:C.28 MBO.16: 5 residues within 4Å: Chain D: K.26, G.27, C.28, N.58, E.60 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:K.26, D:E.60 Metal complexes: D:C.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huber, T.R. et al., Installing Guest Molecules at Specific Sites within Scaffold Protein Crystals. Bioconjug. Chem. (2018)

Release Date

2018-01-03

Peptides

Putative periplasmic protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Putative periplasmic protein

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