SMTL ID : 2v4y.1

THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH ITS ALLOSTERIC REGULATOR GTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

12 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 14 residues within 4Å: Chain A: R.92, D.93, H.96, N.101, A.102, R.103, R.130 Chain E: W.119, A.120, I.123, S.124, R.127 Chain F: N.72, V.75 16 PLIP interactions: 11 interactions with chain A, 3 interactions with chain E, 2 interactions with chain F Hydrogen bonds: A:R.92, A:N.101, A:A.102, E:S.124, E:R.127, E:R.127, F:N.72, F:N.72 Salt bridges: A:D.93, A:H.96, A:H.96, A:R.103, A:R.103, A:R.130, A:R.130 pi-Cation interactions: A:H.96 GTP.2: 8 residues within 4Å: Chain A: S.17, G.18, E.19, G.56, G.57, G.58, T.144, T.145 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.18, A:G.57, A:G.58, A:T.145, A:T.145 Salt bridges: A:K.15 GTP.3: 14 residues within 4Å: Chain A: W.119, A.120, I.123, S.124, R.127 Chain B: R.92, D.93, H.96, N.101, A.102, R.103, R.130 Chain D: N.72, V.75 16 PLIP interactions: 3 interactions with chain A, 13 interactions with chain B Hydrogen bonds: A:S.124, A:R.127, A:R.127, B:R.92, B:D.93, B:N.101, B:N.101, B:A.102, B:R.103 Salt bridges: B:D.93, B:H.96, B:R.103, B:R.103, B:R.130, B:R.130 pi-Cation interactions: B:H.96 GTP.4: 8 residues within 4Å: Chain B: S.17, G.18, E.19, G.56, G.57, G.58, T.144, T.145 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.18, B:E.19, B:E.19, B:G.57, B:G.58, B:T.145, B:T.145, B:T.145, B:T.145 GTP.5: 13 residues within 4Å: Chain C: R.92, D.93, H.96, N.101, A.102, R.103, R.130 Chain E: N.72, V.75 Chain F: W.119, A.120, S.124, R.127 15 PLIP interactions: 3 interactions with chain F, 12 interactions with chain C Hydrogen bonds: F:S.124, F:R.127, F:R.127, C:R.92, C:H.96, C:N.101, C:A.102 Salt bridges: C:D.93, C:H.96, C:H.96, C:R.103, C:R.103, C:R.130, C:R.130 pi-Cation interactions: C:H.96 GTP.6: 9 residues within 4Å: Chain C: K.15, S.17, G.18, E.19, G.56, G.57, G.58, T.144, T.145 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.18, C:E.19, C:E.19, C:G.57, C:G.58, C:T.145, C:T.145, C:T.145, C:T.145 Salt bridges: C:K.15 GTP.7: 14 residues within 4Å: Chain B: N.72, V.75 Chain C: W.119, A.120, I.123, S.124, R.127 Chain D: R.92, D.93, H.96, N.101, A.102, R.103, R.130 16 PLIP interactions: 1 interactions with chain B, 12 interactions with chain D, 3 interactions with chain C Hydrogen bonds: B:N.72, D:R.92, D:D.93, D:H.96, D:N.101, D:A.102, C:S.124, C:R.127, C:R.127 Salt bridges: D:D.93, D:H.96, D:R.103, D:R.103, D:R.130, D:R.130 pi-Cation interactions: D:H.96 GTP.8: 8 residues within 4Å: Chain D: S.17, G.18, E.19, G.56, G.57, G.58, T.144, T.145 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.18, D:E.19, D:G.57, D:G.58, D:T.145, D:T.145, D:T.145 GTP.9: 14 residues within 4Å: Chain B: W.119, A.120, I.123, S.124, R.127 Chain C: N.72, V.75 Chain E: R.92, D.93, H.96, N.101, A.102, R.103, R.130 15 PLIP interactions: 11 interactions with chain E, 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: E:R.92, E:N.101, E:A.102, C:N.72, B:S.124, B:R.127, B:R.127 Salt bridges: E:D.93, E:H.96, E:H.96, E:R.103, E:R.103, E:R.130, E:R.130 pi-Cation interactions: E:H.96 GTP.10: 8 residues within 4Å: Chain E: S.17, G.18, E.19, G.56, G.57, G.58, T.144, T.145 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.18, E:E.19, E:E.19, E:G.57, E:G.58, E:T.145, E:T.145, E:T.145 Salt bridges: E:K.15 GTP.11: 13 residues within 4Å: Chain A: N.72, V.75 Chain D: W.119, A.120, S.124, R.127 Chain F: R.92, D.93, H.96, N.101, A.102, R.103, R.130 15 PLIP interactions: 11 interactions with chain F, 1 interactions with chain A, 3 interactions with chain D Hydrogen bonds: F:R.92, F:H.96, F:N.101, F:A.102, A:N.72, D:S.124, D:R.127, D:R.127 Salt bridges: F:D.93, F:H.96, F:R.103, F:R.103, F:R.130, F:R.130 pi-Cation interactions: F:H.96 GTP.12: 8 residues within 4Å: Chain F: S.17, G.18, E.19, G.56, G.57, G.58, T.144, T.145 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:S.17, F:S.17, F:G.18, F:G.57, F:G.58, F:T.145, F:T.145, F:T.145 Salt bridges: F:K.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meyer, P. et al., Structural and Functional Characterization of Escherichia Coli Ump Kinase in Complex with its Allosteric Regulator GTP. J.Biol.Chem. (2008)

Release Date

2008-10-21

Peptides

URIDYLATE KINASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

URIDYLATE KINASE

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