SMTL ID : 7g86.1

ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1137725943

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

3 x YXB: N-[(1H-indol-4-yl)methyl]ethanamine(Non-covalent)

YXB.1: 4 residues within 4Å: Chain A: P.102, E.103, H.106, F.107 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:H.106 Hydrogen bonds: A:H.106 pi-Stacking: A:F.107 YXB.2: 6 residues within 4Å: Chain A: A.4, D.46, I.47, Q.53, V.54, E.55 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.46, A:Q.53, A:Q.53 Hydrogen bonds: A:E.55 YXB.8: 7 residues within 4Å: Chain A: Y.35 Chain B: M.31, K.32, D.35, V.36, R.197, H.201 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.32, B:K.32, A:Y.35 Hydrogen bonds: B:K.32, B:R.197 Water bridges: B:R.197, B:H.201 pi-Cation interactions: B:R.197

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

DMS.3: 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.4: 4 residues within 4Å: Chain A: F.26, S.27, Y.43, A.45 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.26 DMS.9: 5 residues within 4Å: Chain B: Q.100, A.101, L.102, C.103, P.104 No protein-ligand interaction detected (PLIP) DMS.10: 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.11: 5 residues within 4Å: Chain B: Y.153, A.154, D.156, K.157, Q.160 No protein-ligand interaction detected (PLIP) DMS.12: 2 residues within 4Å: Chain B: L.23, H.26 No protein-ligand interaction detected (PLIP)

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

FMT.5: 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:D.147, 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: 2 residues within 4Å: Chain A: H.106, F.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.107 FMT.13: 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.14: 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.15: 3 residues within 4Å: Chain A: V.36, P.37 Chain B: R.197 No protein-ligand interaction detected (PLIP) FMT.16: 3 residues within 4Å: Chain B: P.192, S.196, K.220 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.220 FMT.17: 5 residues within 4Å: Chain B: C.79, E.82, Q.130, T.134, E.137 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.82, B:Q.130 FMT.18: 2 residues within 4Å: Chain B: K.144, L.233 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.141, B:R.141, B:E.234 FMT.19: 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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