SMTL ID : 6siu.1

Crystal structure of IbpAFic2 covalently tethered to Cdc42

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

hetero-2-2-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.179, L.180, K.184 Chain B: K.51 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.180 Salt bridges: A:R.179, B:K.51 SO4.2: 3 residues within 4Å: Chain A: P.55, E.56 Chain D: Q.75 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:Q.75, A:E.56 Water bridges: D:Q.75, A:A.57 SO4.3: 3 residues within 4Å: Chain A: S.130, R.244 Ligands: LJN.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.130 Salt bridges: A:R.244 SO4.4: 3 residues within 4Å: Chain A: T.160, V.161, Q.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.160, A:V.161, A:Q.162 SO4.5: 4 residues within 4Å: Chain A: K.51 Chain B: R.179, L.180, K.184 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.180 Salt bridges: B:R.179, B:K.184, A:K.51 Water bridges: A:K.51 SO4.6: 3 residues within 4Å: Chain B: P.55, E.56 Chain C: Q.75 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.56, B:A.57, C:Q.75 SO4.7: 3 residues within 4Å: Chain B: T.129, S.130, R.244 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.130, B:S.130 Water bridges: B:T.129, B:T.129, B:R.244, B:R.247 Salt bridges: B:R.244 SO4.8: 3 residues within 4Å: Chain B: T.160, V.161, Q.162 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.160, B:V.161, B:Q.162 SO4.12: 5 residues within 4Å: Chain B: S.280 Chain C: S.87, P.88, S.89, Q.135 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:S.280, B:S.280, C:S.89, C:S.89, C:Q.135 SO4.16: 5 residues within 4Å: Chain A: S.280 Chain D: S.87, P.88, S.89, Q.135 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:S.280, D:S.89, D:S.89, D:S.89, D:Q.135

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

GDP.9: 19 residues within 4Å: Chain B: T.188, E.190, N.191 Chain C: D.12, G.13, A.14, V.15, G.16, K.17, T.18, C.19, F.29, V.34, Q.117, D.119, L.120, S.159, A.160, L.161 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:A.14, C:V.15, C:G.16, C:K.17, C:T.18, C:C.19, C:Q.117, C:Q.117, C:A.160, C:L.161, B:E.190 Water bridges: C:K.17, C:K.17, C:T.18, C:P.35 Salt bridges: C:K.17, C:D.119 pi-Stacking: C:F.29, C:F.29 GDP.13: 17 residues within 4Å: Chain A: E.190, N.191 Chain D: D.12, A.14, V.15, G.16, K.17, T.18, C.19, F.29, V.34, Q.117, D.119, L.120, S.159, A.160, L.161 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:A.14, D:V.15, D:G.16, D:K.17, D:T.18, D:T.18, D:C.19, D:Q.117, D:Q.117, D:S.159, D:A.160, D:L.161 Water bridges: D:K.17, D:K.17, D:T.18, D:T.18, D:D.58 Salt bridges: D:K.17, D:D.119 pi-Stacking: D:F.29, D:F.29

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain B: S.53 Chain C: V.37, T.59, A.60, R.69 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.53, B:S.53, C:A.60 Water bridges: B:S.53 GOL.14: 6 residues within 4Å: Chain A: S.53 Chain D: V.37, T.59, A.60, L.68, R.69 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:A.60, A:S.53 Water bridges: A:S.50

2 x LJN: [(2~{R},3~{S},4~{R},5~{R})-5-[4-(acetamidomethyl)-1,2,3-triazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate(Covalent)

LJN.11: 9 residues within 4Å: Chain B: A.192, Y.229, I.233, G.243, R.247, E.270, I.273, C.274 Chain C: Y.33 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.192 Hydrogen bonds: B:R.247, B:R.247, B:C.274 Water bridges: B:T.129, B:R.244, B:R.247 LJN.15: 15 residues within 4Å: Chain A: A.192, F.194, Y.229, I.233, H.236, E.240, G.241, N.242, G.243, R.247, E.270, I.273, C.274 Chain D: Y.33 Ligands: SO4.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.192, A:F.194 Hydrogen bonds: A:G.241, A:N.242, A:N.242, A:G.243, A:R.247, A:R.247 Salt bridges: A:H.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gulen, B. et al., Identification of targets of AMPylating Fic enzymes by co-substrate-mediated covalent capture. Nat.Chem. (2020)

Release Date

2020-03-18

Peptides

Protein adenylyltransferase 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

Protein adenylyltransferase and cysteine protease IbpA

Cell division control protein 42 homolog