SMTL ID : 2j4j.1

Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UMP and AMPPCP to 2.1 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

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

U5P.1: 17 residues within 4Å: Chain A: G.42, G.43, I.51, D.65, G.68, I.69, G.112, F.113, Q.114, P.115, G.116, Q.117, S.118, T.119, V.122 Ligands: ACP.2, CO.3 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: A:I.69, A:T.119 Hydrogen bonds: A:G.43, A:G.44, A:D.65, A:D.65, A:F.113, A:Q.114, A:Q.114, A:G.116, A:Q.117, A:T.119 Water bridges: A:G.44, A:S.118, F:R.194 Salt bridges: A:K.6 U5P.5: 17 residues within 4Å: Chain B: G.42, G.43, I.51, D.65, G.68, I.69, G.112, F.113, Q.114, P.115, G.116, Q.117, S.118, T.119, V.122 Ligands: ACP.6, CO.7 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.69, B:T.119 Hydrogen bonds: B:G.43, B:D.65, B:F.113, B:Q.114, B:Q.114, B:G.116, B:Q.117, B:T.119, B:T.119 Water bridges: B:S.118 Salt bridges: B:K.6 U5P.9: 19 residues within 4Å: Chain C: G.42, G.43, G.44, A.47, I.51, D.65, G.68, I.69, G.112, F.113, Q.114, P.115, G.116, Q.117, S.118, T.119, V.122 Ligands: ACP.10, CO.11 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.69, C:T.119 Hydrogen bonds: C:G.43, C:G.44, C:D.65, C:D.65, C:F.113, C:Q.114, C:Q.114, C:G.116, C:Q.117, C:T.119, C:T.119 Water bridges: C:Q.117, C:A.120, B:R.194 Salt bridges: C:K.6 U5P.12: 16 residues within 4Å: Chain D: G.42, G.43, D.65, G.68, I.69, G.112, F.113, Q.114, P.115, G.116, Q.117, S.118, T.119, V.122 Ligands: ACP.13, MG.14 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:I.69, D:T.119 Hydrogen bonds: D:G.43, D:G.44, D:D.65, D:D.65, D:F.113, D:Q.114, D:Q.114, D:G.116, D:Q.117, D:T.119 Water bridges: D:A.120 Salt bridges: D:K.6 U5P.15: 16 residues within 4Å: Chain E: G.42, G.43, D.65, G.68, I.69, G.112, F.113, Q.114, P.115, G.116, Q.117, S.118, T.119, V.122 Ligands: ACP.16, CO.17 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:I.69, E:T.119 Hydrogen bonds: E:G.43, E:D.65, E:F.113, E:Q.114, E:Q.114, E:G.116, E:Q.117, E:Q.117, E:T.119, E:T.119 Water bridges: E:G.44, E:A.120 Salt bridges: E:K.6

5 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.2: 23 residues within 4Å: Chain A: K.6, S.8, G.9, K.10, G.43, G.44, R.48, T.139, N.140, V.141, G.143, V.144, Y.145, K.147, D.148, P.149, R.150, I.169, L.170, E.182, L.183 Ligands: U5P.1, CO.3 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:K.6, A:S.8, A:G.9, A:K.10, A:G.43, A:G.44, A:R.48, A:R.48, A:R.48, A:T.139, A:N.140, A:N.140, A:Y.145, A:Y.145, A:E.182, A:L.183 Water bridges: A:G.44, A:T.119, A:T.119, A:D.148, A:D.148, A:R.150 Salt bridges: A:K.6, A:K.10 ACP.6: 24 residues within 4Å: Chain B: K.6, S.8, G.9, K.10, G.42, G.43, G.44, R.48, T.139, N.140, V.141, G.143, V.144, Y.145, K.147, D.148, P.149, R.150, I.169, L.170, E.182, L.183 Ligands: U5P.5, CO.7 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:K.6, B:S.8, B:G.9, B:K.10, B:G.43, B:G.44, B:R.48, B:R.48, B:T.119, B:T.139, B:N.140, B:N.140, B:Y.145, B:Y.145, B:E.182, B:L.183 Water bridges: B:K.10, B:T.119 Salt bridges: B:K.6, B:K.10 ACP.10: 23 residues within 4Å: Chain C: K.6, S.8, G.9, K.10, G.42, G.43, G.44, R.48, T.139, N.140, V.141, G.143, V.144, Y.145, K.147, D.148, P.149, R.150, I.169, L.170, L.183 Ligands: U5P.9, CO.11 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:K.6, C:S.8, C:G.9, C:K.10, C:G.43, C:G.44, C:R.48, C:T.139, C:N.140, C:N.140, C:Y.145, C:Y.145, C:L.183 Water bridges: C:T.119, C:T.119 Salt bridges: C:K.6, C:K.10 ACP.13: 24 residues within 4Å: Chain D: K.6, S.8, G.9, K.10, G.42, G.43, G.44, R.48, T.139, N.140, V.141, G.143, V.144, Y.145, K.147, D.148, P.149, R.150, I.169, L.170, E.182, L.183 Ligands: U5P.12, MG.14 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:K.6, D:S.8, D:G.9, D:K.10, D:G.43, D:G.44, D:R.48, D:T.139, D:N.140, D:N.140, D:Y.145, D:Y.145, D:L.183 Water bridges: D:T.119, D:T.119 Salt bridges: D:K.6, D:K.10 ACP.16: 23 residues within 4Å: Chain E: K.6, S.8, G.9, K.10, G.42, G.43, G.44, R.48, T.139, N.140, V.141, G.143, V.144, Y.145, K.147, D.148, P.149, R.150, I.169, E.182, L.183 Ligands: U5P.15, CO.17 21 PLIP interactions: 21 interactions with chain E Hydrogen bonds: E:K.6, E:S.8, E:G.9, E:K.10, E:G.43, E:G.44, E:R.48, E:R.48, E:T.139, E:N.140, E:N.140, E:Y.145, E:Y.145, E:L.183 Water bridges: E:G.44, E:R.48, E:T.119, E:T.119, E:N.140 Salt bridges: E:K.6, E:K.10

6 x CO: COBALT (II) ION(Non-covalent)(Non-functional Binders)

CO.3: 3 residues within 4Å: Chain A: E.182 Ligands: U5P.1, ACP.2 4 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:E.182, U5P.1, H2O.3, H2O.3 CO.4: 6 residues within 4Å: Chain A: Y.88, H.104 Chain C: Y.88, H.104 Chain E: Y.88, H.104 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain E Metal complexes: A:H.104, C:H.104, E:H.104 CO.7: 2 residues within 4Å: Ligands: U5P.5, ACP.6 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: U5P.5 CO.8: 6 residues within 4Å: Chain B: Y.88, H.104 Chain D: Y.88, H.104 Chain F: Y.88, H.104 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 1 interactions with chain B Metal complexes: D:H.104, F:H.104, B:H.104 CO.11: 2 residues within 4Å: Ligands: U5P.9, ACP.10 2 PLIP interactions: 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.7, U5P.9 CO.17: 3 residues within 4Å: Chain E: E.182 Ligands: U5P.15, ACP.16 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.182

2 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 3 residues within 4Å: Chain D: E.182 Ligands: U5P.12, ACP.13 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:E.182, U5P.12 MG.19: 4 residues within 4Å: Chain F: R.48, T.180, Y.181 Ligands: 4TC.18 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: 4TC.18

1 x 4TC: P1-(5'-ADENOSINE)P4-(5'-URIDINE)-BETA,GAMMA-METHYLENE TETRAPHOSPHATE(Non-covalent)

4TC.18: 39 residues within 4Å: Chain F: K.6, S.8, G.9, K.10, G.42, G.43, G.44, R.48, D.65, G.68, I.69, G.112, F.113, Q.114, P.115, G.116, Q.117, S.118, T.119, V.122, T.139, N.140, V.141, G.143, V.144, Y.145, K.147, D.148, P.149, R.150, I.169, L.170, A.178, G.179, T.180, Y.181, E.182, L.183 Ligands: MG.19 37 PLIP interactions: 35 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:I.69, F:T.119 Hydrogen bonds: F:K.6, F:S.8, F:G.9, F:G.43, F:G.44, F:R.48, F:R.48, F:D.65, F:F.113, F:Q.114, F:Q.114, F:G.116, F:Q.117, F:T.119, F:T.119, F:T.139, F:N.140, F:N.140, F:Y.145, F:Y.145, F:G.179, F:T.180, F:E.182, F:L.183 Water bridges: F:K.10, F:K.10, F:S.118, F:D.148, F:D.148, A:R.194, A:R.194 Salt bridges: F:K.6, F:K.6, F:K.10, F:R.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jensen, K.S. et al., Structural and Enzymatic Investigation of the Sulfolobus Solfataricus Uridylate Kinase Shows Competitive Utp Inhibition and the Lack of GTP Stimulation. Biochemistry (2007)

Release Date

2007-02-27

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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