SMTL ID : 2bmu.1

UMP KINASE FROM PYROCOCCUS FURIOSUS COMPLEXED WITH ITS SUBSTRATE UMP AND ITS SUBSTRATE ANALOG AMPPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-hexamer

Ligands

6 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 25 residues within 4Å: Chain A: G.9, G.10, S.11, G.44, G.45, G.46, R.50, T.121, T.141, N.142, V.143, G.145, V.146, Y.147, A.149, D.150, P.151, K.152, I.171, S.182, S.183, V.184 Ligands: U5P.2, MG.3, MG.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.10, A:S.11, A:S.11, A:S.11, A:G.45, A:G.46, A:R.50, A:R.50, A:T.141, A:N.142, A:N.142, A:Y.147, A:Y.147, A:S.182, A:S.182, A:S.183 Water bridges: A:T.121 ANP.6: 22 residues within 4Å: Chain B: G.9, G.10, S.11, G.44, G.45, G.46, T.121, T.141, N.142, V.143, G.145, V.146, Y.147, A.149, D.150, P.151, S.182, S.183, V.184 Ligands: MG.5, U5P.7, MG.8 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.10, B:S.11, B:G.45, B:G.46, B:T.121, B:T.141, B:N.142, B:N.142, B:Y.147, B:Y.147, B:S.182, B:S.183 Water bridges: B:S.181, B:S.182, B:V.184 ANP.9: 25 residues within 4Å: Chain C: G.9, G.10, S.11, G.44, G.45, G.46, R.50, T.121, T.141, N.142, V.143, G.145, V.146, Y.147, A.149, D.150, P.151, K.152, I.171, S.182, S.183, V.184 Ligands: U5P.10, MG.11, MG.12 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:G.10, C:S.11, C:S.11, C:S.11, C:G.45, C:G.46, C:R.50, C:R.50, C:T.121, C:T.141, C:N.142, C:N.142, C:Y.147, C:Y.147, C:S.182, C:S.182, C:S.183 ANP.14: 22 residues within 4Å: Chain D: G.9, G.10, S.11, G.44, G.45, G.46, T.121, T.141, N.142, V.143, G.145, V.146, Y.147, A.149, D.150, P.151, S.182, S.183, V.184 Ligands: MG.13, U5P.15, MG.16 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:G.10, D:S.11, D:G.45, D:G.46, D:T.141, D:N.142, D:N.142, D:Y.147, D:Y.147, D:S.182, D:S.183 Water bridges: D:I.140, D:S.181, D:S.182, D:V.184 ANP.17: 25 residues within 4Å: Chain E: G.9, G.10, S.11, G.44, G.45, G.46, R.50, T.121, T.141, N.142, V.143, G.145, V.146, Y.147, A.149, D.150, P.151, K.152, I.171, S.182, S.183, V.184 Ligands: U5P.18, MG.19, MG.20 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:G.10, E:S.11, E:S.11, E:S.11, E:G.45, E:G.46, E:R.50, E:R.50, E:T.121, E:T.141, E:N.142, E:N.142, E:Y.147, E:Y.147, E:S.182, E:S.182, E:S.183 ANP.22: 22 residues within 4Å: Chain F: G.9, G.10, S.11, G.44, G.45, G.46, T.121, T.141, N.142, V.143, G.145, V.146, Y.147, A.149, D.150, P.151, S.182, S.183, V.184 Ligands: MG.21, U5P.23, MG.24 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:G.10, F:S.11, F:G.45, F:G.46, F:T.141, F:N.142, F:N.142, F:Y.147, F:Y.147, F:S.182, F:S.183 Water bridges: F:S.181, F:S.182, F:V.184

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

U5P.2: 19 residues within 4Å: Chain A: G.44, G.45, G.46, D.67, G.70, I.71, T.74, G.114, T.115, H.116, P.117, G.118, H.119, T.120, T.121, V.124, A.179, G.180 Ligands: ANP.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.71, A:T.121 Hydrogen bonds: A:G.45, A:G.46, A:D.67, A:D.67, A:T.115, A:H.116, A:H.116, A:G.118, A:T.121, A:G.180 Water bridges: A:T.121, A:T.121 U5P.7: 20 residues within 4Å: Chain B: G.44, G.45, G.46, D.67, G.70, I.71, T.74, G.114, T.115, H.116, P.117, G.118, H.119, T.120, T.121, V.124, A.179, G.180, S.181 Ligands: ANP.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.71, B:T.121 Hydrogen bonds: B:G.45, B:G.46, B:D.67, B:T.115, B:H.116, B:H.116, B:G.118, B:T.120, B:T.120, B:T.121, B:G.180 U5P.10: 19 residues within 4Å: Chain C: G.44, G.45, G.46, D.67, G.70, I.71, T.74, G.114, T.115, H.116, P.117, G.118, H.119, T.120, T.121, V.124, A.179, G.180 Ligands: ANP.9 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.71, C:T.121 Hydrogen bonds: C:G.45, C:G.46, C:D.67, C:T.115, C:H.116, C:H.116, C:G.118, C:T.121, C:G.180 Water bridges: C:T.120, C:D.122 U5P.15: 20 residues within 4Å: Chain D: G.44, G.45, G.46, D.67, G.70, I.71, T.74, G.114, T.115, H.116, P.117, G.118, H.119, T.120, T.121, V.124, A.179, G.180, S.181 Ligands: ANP.14 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.71, D:T.121 Hydrogen bonds: D:G.45, D:G.46, D:D.67, D:T.115, D:H.116, D:H.116, D:G.118, D:T.120, D:T.120, D:T.121, D:G.180 U5P.18: 19 residues within 4Å: Chain E: G.44, G.45, G.46, D.67, G.70, I.71, T.74, G.114, T.115, H.116, P.117, G.118, H.119, T.120, T.121, V.124, A.179, G.180 Ligands: ANP.17 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:I.71, E:T.121 Hydrogen bonds: E:G.45, E:G.46, E:D.67, E:D.67, E:T.115, E:H.116, E:H.116, E:G.118, E:T.121, E:G.180 Water bridges: E:D.122, E:D.122 U5P.23: 20 residues within 4Å: Chain F: G.44, G.45, G.46, D.67, G.70, I.71, T.74, G.114, T.115, H.116, P.117, G.118, H.119, T.120, T.121, V.124, A.179, G.180, S.181 Ligands: ANP.22 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:I.71, F:T.121 Hydrogen bonds: F:G.45, F:G.46, F:D.67, F:D.67, F:T.115, F:H.116, F:H.116, F:G.118, F:T.120, F:T.120, F:T.120, F:T.121, F:G.180

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.7, I.8, G.9, T.121, D.122 Ligands: ANP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.7, A:T.121 MG.4: 3 residues within 4Å: Chain A: D.122, S.183 Ligands: ANP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.122, A:S.183 MG.5: 6 residues within 4Å: Chain B: D.7, G.9, T.121, D.122 Ligands: ANP.6, MG.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.7, B:D.122, H2O.54 MG.8: 6 residues within 4Å: Chain B: D.122, S.183, V.184, I.185 Ligands: MG.5, ANP.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.122, B:S.183, B:V.184 MG.11: 6 residues within 4Å: Chain C: D.7, I.8, G.9, T.121, D.122 Ligands: ANP.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.7, C:T.121 MG.12: 3 residues within 4Å: Chain C: D.122, S.183 Ligands: ANP.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.122, C:S.183 MG.13: 6 residues within 4Å: Chain D: D.7, G.9, T.121, D.122 Ligands: ANP.14, MG.16 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.7, D:D.122, H2O.108 MG.16: 6 residues within 4Å: Chain D: D.122, S.183, V.184, I.185 Ligands: MG.13, ANP.14 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.122, D:S.183, D:V.184 MG.19: 6 residues within 4Å: Chain E: D.7, I.8, G.9, T.121, D.122 Ligands: ANP.17 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.7, E:T.121 MG.20: 3 residues within 4Å: Chain E: D.122, S.183 Ligands: ANP.17 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.122, E:S.183 MG.21: 6 residues within 4Å: Chain F: D.7, G.9, T.121, D.122 Ligands: ANP.22, MG.24 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.7, F:D.122, H2O.162 MG.24: 6 residues within 4Å: Chain F: D.122, S.183, V.184, I.185 Ligands: MG.21, ANP.22 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.122, F:S.183, F:V.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marco-Marin, C. et al., The Crystal Structure of Pyrococcus Furiosus Ump Kinase Provides Insight Into Catalysis and Regulation in Microbial Pyrimidine Nucleotide Biosynthesis. J.Mol.Biol. (2005)

Release Date

2005-07-25

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