SMTL ID : 7g95.1

ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z165170770

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-1-1-mer

Ligands

4 x W0Y: N-methyl-4-sulfamoylbenzamide(Non-covalent)

W0Y.1: 5 residues within 4Å: Chain A: C.21, V.36, P.37, T.38 Chain B: R.197 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.36, A:V.36 Hydrogen bonds: A:T.38 Water bridges: B:R.197, B:R.197 W0Y.2: 10 residues within 4Å: Chain A: R.69, P.72, L.73, Y.75, P.76, F.107 Chain B: S.143, I.230, Q.232 Ligands: FMT.8 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.72, A:F.107 Hydrogen bonds: A:F.107, B:S.143 Water bridges: A:D.77, A:D.77 W0Y.3: 4 residues within 4Å: Chain A: D.46, I.47, E.48, E.173 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.48, A:E.48, A:E.173 W0Y.9: 10 residues within 4Å: Chain B: S.124, G.125, A.128, E.129, C.132, L.218, E.221, L.222, N.225 Ligands: FMT.18 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.128, B:L.218 Hydrogen bonds: B:G.125, B:E.129, B:N.225 Water bridges: B:L.222

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

DMS.4: 3 residues within 4Å: Chain A: R.146, Y.157, E.159 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.146 Salt bridges: A:E.159 DMS.10: 4 residues within 4Å: Chain B: Q.100, A.101, L.102, C.103 No protein-ligand interaction detected (PLIP) DMS.11: 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:H.203, B:I.205 DMS.12: 6 residues within 4Å: Chain B: Y.153, A.154, R.155, D.156, K.157, Q.160 No protein-ligand interaction detected (PLIP) DMS.13: 2 residues within 4Å: Chain B: L.23, H.26 No protein-ligand interaction detected (PLIP)

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

FMT.5: 2 residues within 4Å: Chain A: R.146, N.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.146 Water bridges: A:N.150 FMT.6: 3 residues within 4Å: Chain A: Y.43, V.44 Chain B: R.174 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.43, A:V.44, B:R.174 FMT.7: 4 residues within 4Å: Chain A: E.65, R.71, K.99, W.100 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.14, A:R.71 FMT.8: 3 residues within 4Å: Chain A: H.106, F.107 Ligands: W0Y.2 No protein-ligand interaction detected (PLIP) FMT.14: 3 residues within 4Å: Chain B: H.113, R.114, I.205 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.114 Water bridges: B:H.113, B:H.113 FMT.15: 4 residues within 4Å: Chain B: R.97, 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.16: 2 residues within 4Å: Chain B: P.192, K.220 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.220 Water bridges: B:S.196, B:S.196 FMT.17: 5 residues within 4Å: Chain B: C.79, E.82, K.133, T.134, E.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.82 FMT.18: 4 residues within 4Å: Chain B: I.120, S.124, T.214 Ligands: W0Y.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.124 FMT.19: 2 residues within 4Å: Chain B: K.144, L.233 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.234 FMT.20: 1 residues within 4Å: Chain B: H.113 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.113

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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