SMTL ID : 5xkt.1

Klebsiella pneumoniae UreG in complex with GMPPNP and nickel

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 27 residues within 4Å: Chain A: P.11, V.12, G.13, S.14, G.15, K.16, T.17, A.18, D.45, E.100, G.103, N.147, K.148, D.150, L.151, N.179, L.180, K.181 Chain B: A.125, E.126, G.127, K.129, I.130, K.133, Y.154, V.155 Ligands: NI.2 30 PLIP interactions: 22 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:G.13, A:S.14, A:G.15, A:K.16, A:K.16, A:K.16, A:T.17, A:A.18, A:G.103, A:N.147, A:K.148, A:K.148, A:N.179, A:L.180, A:K.181, A:K.181, B:Y.154 Water bridges: A:D.39, A:D.39, A:K.181, A:K.181, B:K.129, B:K.133, B:K.133, B:K.133, B:K.133, B:V.155 Salt bridges: A:D.150, B:K.129 pi-Cation interactions: A:K.148 GNP.4: 27 residues within 4Å: Chain A: A.125, E.126, G.127, K.129, I.130, K.133, Y.154, V.155 Chain B: P.11, V.12, G.13, S.14, G.15, K.16, T.17, A.18, D.45, E.100, G.103, N.147, K.148, D.150, L.151, N.179, L.180, K.181 Ligands: NI.5 23 PLIP interactions: 7 interactions with chain A, 16 interactions with chain B Hydrogen bonds: A:Y.154, B:G.13, B:G.15, B:K.16, B:K.16, B:T.17, B:A.18, B:G.103, B:N.147, B:K.148, B:K.148, B:N.179, B:L.180, B:K.181 Water bridges: A:K.129, A:K.133, A:K.133, A:K.133, A:V.155, B:K.181 Salt bridges: A:K.129, B:D.150 pi-Cation interactions: B:K.148

3 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 5 residues within 4Å: Chain A: T.17, D.45, E.100 Chain B: K.133 Ligands: GNP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.17, A:D.45, A:E.100, H2O.2 NI.3: 4 residues within 4Å: Chain A: C.68, H.70 Chain B: C.68, H.70 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:C.68, A:H.70, B:C.68, B:H.70 NI.5: 5 residues within 4Å: Chain A: K.133 Chain B: T.17, D.45, E.100 Ligands: GNP.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.17, B:D.45, B:E.100, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuen, M.H. et al., Structural insights into how GTP-dependent conformational changes in a metallochaperone UreG facilitate urease maturation. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-12-13

Peptides

Urease accessory protein UreG: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Urease accessory protein UreG