SMTL ID : 7g8s.1

ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1270393711

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

3 x Z5C: 5-(methoxymethyl)-1,2-oxazole-3-carboxamide(Non-covalent)

Z5C.1: 7 residues within 4Å: Chain A: K.28, P.32, E.33, V.34, Y.35 Chain B: D.12, L.16 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.16 Hydrogen bonds: B:D.12, A:E.33, A:V.34, A:Y.35 Water bridges: A:K.28 Z5C.2: 6 residues within 4Å: Chain A: P.72, Y.75, P.76, D.77, F.107 Ligands: FMT.9 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.72, A:D.77 Water bridges: A:T.78, B:S.143 Z5C.3: 7 residues within 4Å: Chain A: F.26, D.29, D.46, I.47, E.48, R.169, E.173 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.169 Hydrogen bonds: A:E.48, A:E.48, A:E.173

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: 3 residues within 4Å: Chain B: Q.100, A.101, L.102 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)

13 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: 1 residues within 4Å: Chain A: P.109 No protein-ligand interaction detected (PLIP) FMT.8: 4 residues within 4Å: Chain A: R.71, K.99, W.100, E.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.103 FMT.9: 3 residues within 4Å: Chain A: H.106, F.107 Ligands: Z5C.2 No protein-ligand interaction detected (PLIP) FMT.14: 4 residues within 4Å: Chain B: H.113, R.114, I.205 Ligands: FMT.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.114 Water bridges: B:H.113 FMT.15: 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.16: 3 residues within 4Å: Chain A: V.36, P.37 Chain B: R.197 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.36 FMT.17: 3 residues within 4Å: Chain B: P.192, S.196, K.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.196, B:K.220 FMT.18: 4 residues within 4Å: Chain B: C.79, E.82, K.133, T.134 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.82 FMT.19: 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.20: 2 residues within 4Å: Chain B: K.144, L.233 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.234 FMT.21: 2 residues within 4Å: Chain B: H.113 Ligands: FMT.14 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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