SMTL ID : 4cry.1

Direct visualisation of strain-induced protein post-translational modification

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.1: 25 residues within 4Å: Chain B: W.23, E.25, Y.26, S.65, L.66, R.67, V.68, R.73, R.74, R.75, G.76, V.77, G.78, Q.79, A.100, G.101, V.102, E.103, V.107, M.108, A.110, F.111, A.114 Chain C: R.78 Ligands: MG.2 23 PLIP interactions: 22 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:E.25, B:Y.26, B:L.66 Hydrogen bonds: B:L.66, B:V.68, B:R.74, B:R.74, B:G.76, B:G.76, B:V.77, B:G.78, B:Q.79, B:E.103, B:E.103 Water bridges: B:R.67, B:R.73, B:Q.79, B:E.103, B:D.104 Salt bridges: B:R.74, C:R.78 pi-Cation interactions: B:R.74, B:R.74 ACO.4: 25 residues within 4Å: Chain E: W.23, E.25, Y.26, S.65, L.66, R.67, V.68, R.73, R.74, R.75, G.76, V.77, G.78, Q.79, A.100, G.101, V.102, E.103, V.107, M.108, A.110, F.111, A.114 Chain F: R.78 Ligands: MG.5 23 PLIP interactions: 22 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:E.25, E:Y.26, E:L.66 Hydrogen bonds: E:L.66, E:V.68, E:R.74, E:R.74, E:G.76, E:G.76, E:V.77, E:G.78, E:Q.79, E:E.103, E:E.103 Water bridges: E:R.67, E:R.73, E:Q.79, E:E.103, E:D.104 Salt bridges: E:R.74, F:R.78 pi-Cation interactions: E:R.74, E:R.74 ACO.7: 25 residues within 4Å: Chain H: W.23, E.25, Y.26, S.65, L.66, R.67, V.68, R.73, R.74, R.75, G.76, V.77, G.78, Q.79, A.100, G.101, V.102, E.103, V.107, M.108, A.110, F.111, A.114 Chain I: R.78 Ligands: MG.8 23 PLIP interactions: 22 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:E.25, H:Y.26, H:L.66 Hydrogen bonds: H:L.66, H:V.68, H:R.74, H:R.74, H:G.76, H:G.76, H:V.77, H:G.78, H:Q.79, H:E.103, H:E.103 Water bridges: H:R.67, H:R.73, H:Q.79, H:E.103, H:D.104 Salt bridges: H:R.74, I:R.78 pi-Cation interactions: H:R.74, H:R.74 ACO.10: 25 residues within 4Å: Chain K: W.23, E.25, Y.26, S.65, L.66, R.67, V.68, R.73, R.74, R.75, G.76, V.77, G.78, Q.79, A.100, G.101, V.102, E.103, V.107, M.108, A.110, F.111, A.114 Chain L: R.78 Ligands: MG.11 23 PLIP interactions: 22 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:E.25, K:Y.26, K:L.66 Hydrogen bonds: K:L.66, K:V.68, K:R.74, K:R.74, K:G.76, K:G.76, K:V.77, K:G.78, K:Q.79, K:E.103, K:E.103 Water bridges: K:R.67, K:R.73, K:Q.79, K:E.103, K:D.104 Salt bridges: K:R.74, L:R.78 pi-Cation interactions: K:R.74, K:R.74

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain B: T.72, R.73, R.74, R.75, G.76, V.77 Ligands: ACO.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.72 MG.5: 7 residues within 4Å: Chain E: T.72, R.73, R.74, R.75, G.76, V.77 Ligands: ACO.4 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.72 MG.8: 7 residues within 4Å: Chain H: T.72, R.73, R.74, R.75, G.76, V.77 Ligands: ACO.7 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.72 MG.11: 7 residues within 4Å: Chain K: T.72, R.73, R.74, R.75, G.76, V.77 Ligands: ACO.10 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.72

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain L: T.68 Ligands: CL.6, CL.9, CL.12 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain I: T.68 Ligands: CL.3, CL.9, CL.12 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain F: T.68 Ligands: CL.3, CL.6, CL.12 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain C: T.68 Ligands: CL.3, CL.6, CL.9 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Monteiro, D.C.F. et al., Direct Visualisation of Strain-Induced Protein Post-Translational Modification. To be Published

Release Date

2015-03-25

Peptides

ASPARTATE 1-DECARBOXYLASE: ADGJ
PANZ: BEHK
ASPARTATE 1-DECARBOXYLASE: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

B
B

E
B

H
B

K
B

C
G

F
G

I
G

L
G

ASPARTATE 1-DECARBOXYLASE

PANZ

ASPARTATE 1-DECARBOXYLASE

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