SMTL ID : 7g82.1

ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1079512010

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

hetero-1-1-mer

Ligands

3 x UWS: 6-methyl-2-[(3-methyl-1,2-oxazol-5-yl)methyl]pyridazin-3(2H)-one(Non-covalent)

UWS.1: 5 residues within 4Å: Chain A: R.123, N.124, K.141, P.142 Ligands: DMS.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.141, A:P.142, A:P.142 Hydrogen bonds: A:N.124 pi-Cation interactions: A:R.123 UWS.2: 6 residues within 4Å: Chain A: E.98, K.99, P.102, E.103, H.106, F.107 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.102, A:H.106 UWS.11: 6 residues within 4Å: Chain B: Y.231, I.242, Y.243, N.244, R.245 Ligands: FMT.23 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.231, B:I.242 Hydrogen bonds: B:Y.231 pi-Stacking: B:Y.231

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

DMS.3: 4 residues within 4Å: Chain A: R.146, Y.157, E.159 Ligands: UWS.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.146 Salt bridges: A:E.159 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.204 Water bridges: B:H.203, B:I.205 DMS.14: 3 residues within 4Å: Chain B: L.23, H.26, K.28 No protein-ligand interaction detected (PLIP) DMS.15: 2 residues within 4Å: Chain B: R.238, L.239 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.239

15 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: 2 residues within 4Å: Chain A: P.109, V.111 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.110 FMT.7: 2 residues within 4Å: Chain A: K.99, W.100 No protein-ligand interaction detected (PLIP) FMT.8: 2 residues within 4Å: Chain A: H.106, F.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.107 FMT.9: 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.10: 6 residues within 4Å: Chain A: K.8, W.59, P.76 Chain B: Q.178, E.179, L.182 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.76 Water bridges: A:K.8 FMT.16: 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.17: 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.18: 3 residues within 4Å: Chain A: V.36, P.37 Chain B: R.197 No protein-ligand interaction detected (PLIP) FMT.19: 3 residues within 4Å: Chain B: P.192, L.193, K.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.196, B:K.220 FMT.20: 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.21: 2 residues within 4Å: Chain B: K.144, L.233 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.234 FMT.22: 1 residues within 4Å: Chain B: H.113 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.113 FMT.23: 5 residues within 4Å: Chain A: R.69 Chain B: I.230, Y.231, R.245 Ligands: UWS.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.245, B:R.245

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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