SMTL ID : 7g8k.1

ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1217131798

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

hetero-1-1-mer

Ligands

3 x YZK: (3M)-3-(2-methyl-1H-imidazol-1-yl)pyridine(Non-covalent)

YZK.1: 8 residues within 4Å: Chain A: P.72, L.73, Y.75, P.76, F.107 Chain B: K.147, Q.232 Ligands: FMT.9 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:D.77, A:D.77, B:Q.232 pi-Stacking: A:F.107 YZK.2: 6 residues within 4Å: Chain A: D.68, P.72, P.102, E.103, H.106, F.107 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:F.107 YZK.11: 5 residues within 4Å: Chain A: V.34 Chain B: S.15, L.23, M.31 Ligands: DMS.15 No protein-ligand interaction detected (PLIP)

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

DMS.3: 4 residues within 4Å: Chain A: R.146, Y.157, E.159 Ligands: FMT.10 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: 5 residues within 4Å: Chain B: Y.153, A.154, D.156, K.157, Q.160 No protein-ligand interaction detected (PLIP) DMS.15: 4 residues within 4Å: Chain B: L.23, Q.24, H.26 Ligands: YZK.11 No protein-ligand interaction detected (PLIP) DMS.16: 2 residues within 4Å: Chain B: R.238, L.239 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.239 Water bridges: B:Q.240

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

FMT.4: 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.5: 2 residues within 4Å: Chain A: P.37 Chain B: R.197 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.37 FMT.6: 3 residues within 4Å: Chain A: Y.43, V.44 Chain B: R.174 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.44, B:R.174 FMT.7: 2 residues within 4Å: Chain A: P.109, V.111 No protein-ligand interaction detected (PLIP) FMT.8: 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.9: 2 residues within 4Å: Chain A: H.106 Ligands: YZK.1 No protein-ligand interaction detected (PLIP) FMT.10: 2 residues within 4Å: Chain A: P.142 Ligands: DMS.3 No protein-ligand interaction detected (PLIP) FMT.17: 4 residues within 4Å: Chain B: H.113, R.114, I.205 Ligands: FMT.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.114 Water bridges: B:H.113 FMT.18: 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.19: 3 residues within 4Å: Chain B: P.192, S.196, K.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.220 Water bridges: B:S.196 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: 3 residues within 4Å: Chain B: I.120, S.124, T.214 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.124, B:S.124 FMT.22: 2 residues within 4Å: Chain B: K.144, L.233 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.234 FMT.23: 2 residues within 4Å: Chain B: H.113 Ligands: FMT.17 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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