SMTL ID : 3kyg.1

Crystal structure of VCA0042 (L135R) complexed with c-di-GMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

8 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.1: 10 residues within 4Å: Chain A: R.116, R.120, R.149, C.187, N.188, Q.190 Chain B: S.192 Ligands: 5GP.2, 5GP.3, 5GP.4 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.116, A:R.120, A:R.120, A:R.149, A:N.188, A:Q.190, B:S.192, B:S.192 Water bridges: A:R.116, A:R.149 Salt bridges: A:R.116, A:R.149 5GP.2: 7 residues within 4Å: Chain A: R.79, G.80, Q.114, R.115, R.116 Ligands: 5GP.1, 5GP.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.80, A:Q.114, A:R.115, A:R.116, A:R.116 Water bridges: A:E.81, A:G.82, A:G.82, A:R.116 pi-Cation interactions: A:R.116, A:R.116 5GP.3: 14 residues within 4Å: Chain A: R.120, D.142, S.144, S.146, G.147, C.148, R.149, C.187, N.188, G.199, L.200, E.201 Ligands: 5GP.1, 5GP.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.120, A:R.120, A:S.144, A:S.144, A:S.144, A:S.144, A:R.149, A:N.188 Water bridges: A:S.146, A:S.146 Salt bridges: A:D.142 pi-Cation interactions: A:R.120, A:R.120 5GP.4: 9 residues within 4Å: Chain A: G.80, E.81, R.115, R.116, K.117, R.120 Ligands: 5GP.1, 5GP.2, 5GP.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.115, A:R.115, A:R.115, A:R.116, A:K.117, A:R.120 Water bridges: A:E.81, A:E.118 Salt bridges: A:E.81, A:R.120 5GP.5: 10 residues within 4Å: Chain A: S.192, H.194 Chain B: R.116, R.120, R.149, N.188, Q.190 Ligands: 5GP.6, 5GP.7, 5GP.8 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.116, B:R.120, B:R.120, B:R.149, B:R.149, B:N.188, B:Q.190, A:S.192, A:S.192 Water bridges: B:R.116, B:R.116, B:R.149 Salt bridges: B:R.116, B:R.149 5GP.6: 7 residues within 4Å: Chain B: R.79, G.80, Q.114, R.115, R.116 Ligands: 5GP.5, 5GP.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.80, B:Q.114, B:R.115, B:R.116, B:R.116 Water bridges: B:R.116 pi-Cation interactions: B:R.116, B:R.116 5GP.7: 15 residues within 4Å: Chain A: H.194 Chain B: R.120, D.142, S.144, S.146, G.147, C.148, R.149, C.187, N.188, G.199, L.200, E.201 Ligands: 5GP.5, 5GP.8 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.120, B:R.120, B:S.144, B:S.144, B:S.144, B:S.144, B:R.149, B:N.188 Water bridges: B:K.117, B:E.118, B:S.146 Salt bridges: B:D.142, A:H.194 pi-Cation interactions: B:R.120 5GP.8: 10 residues within 4Å: Chain A: H.194 Chain B: G.80, E.81, R.115, R.116, K.117, R.120 Ligands: 5GP.5, 5GP.6, 5GP.7 14 PLIP interactions: 2 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:H.194, B:R.115, B:R.115, B:R.115, B:R.116, B:K.117, B:R.120 Water bridges: A:H.195, B:E.81, B:E.81, B:E.81, B:E.118 Salt bridges: B:E.81, B:R.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ko, J. et al., Structure of PP4397 Reveals the Molecular Basis for Different c-di-GMP Binding Modes by Pilz Domain Proteins. J.Mol.Biol. (2010)

Release Date

2010-04-14

Peptides

Putative uncharacterized protein VCA0042: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative uncharacterized protein VCA0042