SMTL ID : 7g8l.1

ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1251207602

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

4 x RWS: 1-(5-methyl-1,3,4-thiadiazol-2-yl)piperidine(Non-covalent)

RWS.1: 6 residues within 4Å: Chain A: D.68, R.71, P.102, E.103, H.106, F.107 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.68, A:P.102 pi-Stacking: A:F.107 RWS.2: 5 residues within 4Å: Chain A: V.25, F.31, P.32, V.36, K.163 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.25, A:P.32, A:V.36 RWS.10: 6 residues within 4Å: Chain A: V.36, P.37 Chain B: L.193, S.196, R.197, Q.200 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.36 pi-Cation interactions: B:R.197 RWS.11: 5 residues within 4Å: Chain A: V.34 Chain B: S.15, L.16, L.23, M.31 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.16, A:V.34 Hydrogen bonds: B:S.15

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.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, H.26, K.28, M.31 No protein-ligand interaction detected (PLIP) DMS.16: 2 residues within 4Å: Chain B: R.238, L.239 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.239

13 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 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.6: 2 residues within 4Å: Chain A: P.109, V.111 No protein-ligand interaction detected (PLIP) FMT.7: 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:R.71 FMT.8: 1 residues within 4Å: Chain A: H.106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.107 FMT.9: 4 residues within 4Å: Chain A: P.72, L.73, P.76, F.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.143 FMT.17: 3 residues within 4Å: Chain B: H.113, R.114, I.205 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.114 Water bridges: B:H.113 FMT.18: 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.19: 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.20: 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.21: 2 residues within 4Å: Chain B: I.120, S.124 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.124 FMT.22: 3 residues within 4Å: Chain B: K.144, L.233, E.234 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.234 FMT.23: 1 residues within 4Å: Chain B: H.113 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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