SMTL ID : 7g85.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

hetero-1-1-mer

Ligands

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

LXA.1: 7 residues within 4Å: Chain A: V.25, F.26, S.27, D.29, Y.43, V.168, R.169 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.26, A:S.27, A:D.29 LXA.9: 9 residues within 4Å: Chain A: E.33, V.34, Y.35 Chain B: M.31, K.32, D.35, R.197, H.201 Ligands: DMS.3 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:K.32, B:K.32, A:Y.35 Hydrogen bonds: B:D.35, A:V.34

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

DMS.2: 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.3: 6 residues within 4Å: Chain A: F.31, P.32, V.34, Y.35, V.36 Ligands: LXA.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.36 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: 3 residues within 4Å: Chain B: L.23, H.26, M.31 No protein-ligand interaction detected (PLIP)

13 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: 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.6: 2 residues within 4Å: Chain A: N.110, 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:D.14 FMT.8: 3 residues within 4Å: Chain A: H.106, F.107, P.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.107 FMT.14: 3 residues within 4Å: Chain B: H.113, R.114, I.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.114 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 No protein-ligand interaction detected (PLIP) FMT.17: 4 residues within 4Å: Chain B: P.192, L.193, S.196, K.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.196, B:K.220 FMT.18: 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.19: 2 residues within 4Å: Chain B: I.120, S.124 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 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.141, B:E.234 FMT.21: 1 residues within 4Å: Chain B: H.113 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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