SMTL ID : 7g8g.1

ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z111529496

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

hetero-1-1-mer

Ligands

2 x LXA: ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-2-methoxy-ethanamide(Non-covalent)

LXA.1: 8 residues within 4Å: Chain A: E.33, V.34, Y.35 Chain B: M.31, K.32, D.35, R.197, H.201 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.35, B:K.32, B:K.32 Hydrogen bonds: A:V.34 LXA.2: 6 residues within 4Å: Chain A: T.20, C.21, V.36, P.37, T.38 Chain B: R.197 No protein-ligand interaction detected (PLIP)

5 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.9: 3 residues within 4Å: Chain B: Q.100, A.101, L.102 No protein-ligand interaction detected (PLIP) DMS.10: 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.11: 5 residues within 4Å: Chain B: A.154, R.155, D.156, K.157, Q.160 No protein-ligand interaction detected (PLIP) DMS.12: 3 residues within 4Å: Chain B: L.23, H.26, K.28 No protein-ligand interaction detected (PLIP)

12 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: 3 residues within 4Å: Chain A: E.65, K.99, W.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.65 Water bridges: A:R.71 FMT.7: 1 residues within 4Å: Chain A: H.106 No protein-ligand interaction detected (PLIP) FMT.8: 4 residues within 4Å: Chain A: P.72, L.73, P.76, F.107 No protein-ligand interaction detected (PLIP) FMT.13: 4 residues within 4Å: Chain B: H.113, R.114, I.205 Ligands: FMT.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.113, B:R.114 FMT.14: 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.15: 4 residues within 4Å: Chain B: P.192, S.196, L.216, K.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.196, B:K.220 FMT.16: 3 residues within 4Å: Chain B: C.79, E.82, K.133 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.82, B:K.133 FMT.17: 1 residues within 4Å: Chain B: T.214 No protein-ligand interaction detected (PLIP) FMT.18: 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.19: 3 residues within 4Å: Chain B: H.113, I.205 Ligands: FMT.13 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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