SMTL ID : 7g8b.1

ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z100643660

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

hetero-1-1-mer

Ligands

4 x LFO: N,1-dimethyl-1H-indole-3-carboxamide(Non-covalent)

LFO.1: 7 residues within 4Å: Chain A: D.68, R.71, P.102, E.103, H.106, F.107 Ligands: FMT.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:H.106 pi-Stacking: A:H.106 LFO.2: 3 residues within 4Å: Chain A: D.147, N.150, R.151 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.147, A:N.150, A:R.151, A:R.151 LFO.10: 5 residues within 4Å: Chain A: V.36, P.37, T.38 Chain B: R.197, Q.200 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.197, A:T.38 Hydrogen bonds: B:Q.200 Water bridges: B:R.197 pi-Cation interactions: B:R.197 LFO.11: 6 residues within 4Å: Chain B: G.125, A.128, E.129, C.132, L.222, N.225 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.128, B:E.129

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 2 residues within 4Å: Chain A: R.146, Y.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.146 Salt bridges: A:E.159 DMS.12: 4 residues within 4Å: Chain B: Q.100, A.101, L.102, C.103 No protein-ligand interaction detected (PLIP) DMS.13: 7 residues within 4Å: Chain B: E.29, V.30, Q.33, H.201, S.202, H.203, G.204 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.204 Water bridges: B:Q.33, B:H.203 DMS.14: 2 residues within 4Å: Chain B: L.23, H.26 No protein-ligand interaction detected (PLIP)

14 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 2 residues within 4Å: Chain A: R.146, N.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.146 Water bridges: A:R.146, A:N.150 FMT.5: 3 residues within 4Å: Chain A: Y.43, V.44 Chain B: R.174 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.174, A:V.44 FMT.6: 3 residues within 4Å: Chain A: K.99, W.100, E.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.103 Water bridges: A:D.14 FMT.7: 3 residues within 4Å: Chain A: H.106, F.107, P.109 No protein-ligand interaction detected (PLIP) FMT.8: 5 residues within 4Å: Chain A: P.72, L.73, P.76, F.107 Chain B: S.143 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.143 FMT.9: 5 residues within 4Å: Chain A: D.68, R.69, P.72, F.107 Ligands: LFO.1 No protein-ligand interaction detected (PLIP) FMT.15: 3 residues within 4Å: Chain B: H.113, R.114, I.205 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.114 Water bridges: B:H.113 FMT.16: 5 residues within 4Å: Chain B: R.97, V.111, I.112, H.113, R.114 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.97, B:H.113, B:R.114 FMT.17: 2 residues within 4Å: Chain B: P.104, G.105 No protein-ligand interaction detected (PLIP) FMT.18: 4 residues within 4Å: Chain B: P.192, L.193, S.196, K.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.220 Water bridges: B:S.196 FMT.19: 4 residues within 4Å: Chain B: C.79, E.82, T.134, E.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.82 FMT.20: 4 residues within 4Å: Chain B: I.120, S.124, T.214, L.218 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.124, B:S.124 FMT.21: 2 residues within 4Å: Chain B: K.144, L.233 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.141, B:E.234 FMT.22: 1 residues within 4Å: Chain B: H.113 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bradshaw, W.J. et al., ARHGEF2 PanDDA analysis group deposition. To Be Published

Release Date

2023-07-12

Peptides

Transforming protein RhoA: A
Rho guanine nucleotide exchange factor 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transforming protein RhoA

Rho guanine nucleotide exchange factor 2

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