SMTL ID : 2bne.1

The structure of E. coli UMP kinase in complex with UMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

6 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.1: 19 residues within 4Å: Chain A: G.56, G.57, G.58, F.61, R.62, G.63, D.77, G.80, M.81, T.84, G.137, T.138, G.139, N.140, P.141, F.142, F.143, T.144, T.145 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.57, A:G.58, A:R.62, A:G.63, A:D.77, A:T.138, A:G.139, A:N.140, A:F.142, A:F.143, A:T.145 Water bridges: A:K.15, A:K.15, A:G.18, A:A.64, A:D.77 U5P.6: 18 residues within 4Å: Chain B: G.56, G.57, G.58, F.61, R.62, G.63, D.77, G.80, M.81, T.84, G.137, T.138, G.139, N.140, P.141, F.143, T.144, T.145 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:T.145 Hydrogen bonds: B:G.57, B:G.58, B:R.62, B:G.63, B:D.77, B:D.77, B:T.138, B:G.139, B:N.140, B:T.145, B:T.145 Water bridges: B:K.15, B:A.64, B:F.143 U5P.10: 19 residues within 4Å: Chain C: G.56, G.57, G.58, F.61, R.62, G.63, D.77, G.80, M.81, T.84, G.137, T.138, G.139, N.140, P.141, F.142, F.143, T.144, T.145 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:G.57, C:G.58, C:R.62, C:G.63, C:D.77, C:T.138, C:G.139, C:N.140, C:F.142, C:F.143, C:T.145 Water bridges: C:K.15, C:K.15, C:G.18, C:A.64, C:D.77 U5P.15: 18 residues within 4Å: Chain D: G.56, G.57, G.58, F.61, R.62, G.63, D.77, G.80, M.81, T.84, G.137, T.138, G.139, N.140, P.141, F.143, T.144, T.145 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:T.145 Hydrogen bonds: D:G.57, D:G.58, D:R.62, D:G.63, D:D.77, D:D.77, D:T.138, D:G.139, D:N.140, D:T.145, D:T.145 Water bridges: D:K.15, D:A.64, D:F.143 U5P.19: 19 residues within 4Å: Chain E: G.56, G.57, G.58, F.61, R.62, G.63, D.77, G.80, M.81, T.84, G.137, T.138, G.139, N.140, P.141, F.142, F.143, T.144, T.145 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:G.57, E:G.58, E:R.62, E:G.63, E:D.77, E:T.138, E:G.139, E:N.140, E:F.142, E:F.143, E:T.145 Water bridges: E:K.15, E:K.15, E:G.18, E:A.64, E:D.77 U5P.24: 18 residues within 4Å: Chain F: G.56, G.57, G.58, F.61, R.62, G.63, D.77, G.80, M.81, T.84, G.137, T.138, G.139, N.140, P.141, F.143, T.144, T.145 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:T.145 Hydrogen bonds: F:G.57, F:G.58, F:R.62, F:G.63, F:D.77, F:D.77, F:T.138, F:G.139, F:N.140, F:T.145, F:T.145 Water bridges: F:K.15, F:A.64, F:F.143

21 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: Q.39, K.42 Ligands: GOL.3 Ligand excluded by PLIP GOL.3: 4 residues within 4Å: Chain A: Q.39, E.43, E.46 Ligands: GOL.2 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: V.192, L.193, E.196, L.197, V.199, M.200, L.202 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: H.96, Y.99, V.100, N.101 Chain C: R.127 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain B: R.73 Chain C: D.210, H.211 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain B: Q.39, E.40, E.43, R.227 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain B: K.10, Q.50, R.127, N.129 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain C: Q.39, K.42 Ligands: GOL.12 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain C: Q.39, E.43, E.46 Ligands: GOL.11 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain C: V.192, L.193, E.196, L.197, V.199, M.200, L.202 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain C: H.96, Y.99, V.100, N.101 Chain E: R.127 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain D: R.73 Chain E: D.210, H.211 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain D: Q.39, E.40, E.43, R.227 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain D: K.10, Q.50, R.127, N.129 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain E: Q.39, K.42 Ligands: GOL.21 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain E: Q.39, E.43, E.46 Ligands: GOL.20 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain E: V.192, L.193, E.196, L.197, V.199, M.200, L.202 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain A: R.127 Chain E: H.96, Y.99, V.100, N.101 Ligand excluded by PLIP GOL.25: 3 residues within 4Å: Chain A: D.210, H.211 Chain F: R.73 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain F: Q.39, E.40, E.43, R.227 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain F: K.10, Q.50, R.127, N.129 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Briozzo, P. et al., Structure of Escherichia Coli Ump Kinase Differs from that of Other Nucleoside Monophosphate Kinases and Sheds New Light on Enzyme Regulation. J.Biol.Chem. (2005)

Release Date

2005-04-25

Peptides

URIDYLATE KINASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

URIDYLATE KINASE

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