SMTL ID : 7g99.1

ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with PCM-0102102-001

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ZE9: 1-[(3R,5R)-5-(furan-2-yl)-3-(5-methylfuran-2-yl)pyrazolidin-1-yl]ethan-1-one(Covalent)

ZE9.1: 8 residues within 4Å: Chain A: C.21, V.25, F.31, V.36, A.162, K.163 Chain B: R.197 Ligands: FMT.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.31, A:V.36 Water bridges: A:K.119 ZE9.11: 5 residues within 4Å: Chain B: E.129, C.132, K.133, N.225, E.228 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.228 Hydrogen bonds: B:K.133

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

DMS.2: 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.3: 3 residues within 4Å: Chain A: F.26, A.45, D.46 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.46 DMS.4: 5 residues within 4Å: Chain A: K.8, W.59, P.76 Chain B: Q.178, L.182 No protein-ligand interaction detected (PLIP) DMS.12: 3 residues within 4Å: Chain B: Q.100, A.101, L.102 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 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.204 Water bridges: B:I.205 DMS.14: 5 residues within 4Å: Chain B: L.23, Q.24, H.26, K.28, M.31 No protein-ligand interaction detected (PLIP)

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

FMT.5: 1 residues within 4Å: Chain A: R.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.146 FMT.6: 5 residues within 4Å: Chain A: V.36, P.37, T.38 Chain B: R.197 Ligands: ZE9.1 No protein-ligand interaction detected (PLIP) FMT.7: 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.8: 4 residues within 4Å: Chain A: R.71, K.99, W.100, E.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.71, A:E.103 Water bridges: A:D.14 FMT.9: 1 residues within 4Å: Chain A: H.106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.106 FMT.10: 3 residues within 4Å: Chain A: P.72, F.107 Chain B: S.143 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.143 FMT.15: 4 residues within 4Å: Chain B: H.113, R.114, I.205 Ligands: FMT.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.114 FMT.16: 5 residues within 4Å: Chain B: R.97, V.111, I.112, H.113, R.114 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.113, B:R.114 Water bridges: B:V.111, B:H.113 FMT.17: 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:S.196, B:K.220 FMT.18: 2 residues within 4Å: Chain B: C.79, E.82 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.82 FMT.19: 2 residues within 4Å: Chain B: S.124, T.214 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.124, B:S.124 FMT.20: 3 residues within 4Å: Chain B: K.144, L.233, E.234 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.234, B:E.234 FMT.21: 2 residues within 4Å: Chain B: H.113 Ligands: FMT.15 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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