SMTL ID : 4itr.1

Crystal Structure of IbpAFic2-H3717A in complex with adenylylated Cdc42

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.179, L.180 Chain B: K.51 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.180 Water bridges: A:R.179, A:R.179, A:K.184 Salt bridges: A:R.179, A:K.184, B:K.51 SO4.2: 3 residues within 4Å: Chain A: K.51 Chain B: R.179, L.180 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Salt bridges: A:K.51, B:R.179, B:K.184 Hydrogen bonds: B:L.180 Water bridges: B:R.179, B:K.184 SO4.6: 6 residues within 4Å: Chain B: K.278, S.280 Chain C: S.86, P.87, S.88, Q.134 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:S.88, C:S.88, C:S.88, C:Q.134 Water bridges: C:S.86, C:S.86, B:K.278, B:K.278 Salt bridges: B:K.278 SO4.10: 6 residues within 4Å: Chain A: K.278, S.280 Chain D: S.86, P.87, S.88, Q.134 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:S.88, D:S.88, D:Q.134 Water bridges: A:K.278, A:K.278, A:K.278 Salt bridges: A:K.278

2 x AMP: ADENOSINE MONOPHOSPHATE(Covalent)

AMP.3: 15 residues within 4Å: Chain B: K.189, E.190, A.192, I.233, E.240, G.241, N.242, G.243, R.247, K.264, E.270, P.271, I.274, Q.276 Chain C: Y.32 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:E.240, B:N.242, B:N.242, B:G.243, B:R.247, B:R.247, B:K.264, B:Q.276, B:Q.276 Water bridges: B:N.191, B:G.241, B:G.241 Salt bridges: B:K.189 AMP.7: 14 residues within 4Å: Chain A: K.189, E.190, A.192, I.233, E.240, G.241, N.242, G.243, R.247, E.270, P.271, I.274, Q.276 Chain D: Y.32 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.241, A:N.242, A:N.242, A:G.243, A:R.247, A:R.247, A:K.264, A:Q.276, A:Q.276 Water bridges: A:N.191, A:Y.229, A:K.264 Salt bridges: A:K.189

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.4: 18 residues within 4Å: Chain B: E.190, N.191 Chain C: D.11, G.12, A.13, V.14, G.15, K.16, T.17, C.18, F.28, Q.116, D.118, L.119, S.158, A.159, L.160 Ligands: MG.5 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:A.13, C:V.14, C:G.15, C:K.16, C:T.17, C:C.18, C:Q.116, C:Q.116, C:S.158, C:A.159, C:L.160, B:E.190 Water bridges: C:T.17, C:T.17, C:P.29, C:T.35, C:Q.61 Salt bridges: C:K.16, C:D.118 pi-Stacking: C:F.28, C:F.28 GDP.8: 18 residues within 4Å: Chain A: E.190, N.191 Chain D: D.11, A.13, V.14, G.15, K.16, T.17, C.18, F.28, V.33, Q.116, D.118, L.119, S.158, A.159, L.160 Ligands: MG.9 23 PLIP interactions: 22 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:D.11, D:A.13, D:V.14, D:G.15, D:K.16, D:T.17, D:T.17, D:C.18, D:Q.116, D:Q.116, D:A.159, D:L.160, A:E.190 Water bridges: D:T.17, D:T.17, D:L.19, D:T.35, D:T.35, D:Q.61 Salt bridges: D:K.16, D:D.118 pi-Stacking: D:F.28, D:F.28

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain C: T.17, T.35, D.57 Ligands: GDP.4 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.17, C:T.35, H2O.22, H2O.23 MG.9: 4 residues within 4Å: Chain D: T.17, T.35, D.57 Ligands: GDP.8 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.17, D:T.35, H2O.28, H2O.29, H2O.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, J. et al., Structural basis of Fic-mediated adenylylation. Nat.Struct.Mol.Biol. (2010)

Release Date

2013-02-20

Peptides

Adenosine monophosphate-protein transferase and cysteine protease IbpA: AB
Cell division control protein 42 homolog: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Adenosine monophosphate-protein transferase and cysteine protease IbpA

Cell division control protein 42 homolog

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