SMTL ID : 8yh1.1 (1 other biounit)

Crystal structure of Thermus thermophilus UMP kinase complexed with a phosphoryl group acceptor and donor.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 18 residues within 4Å: Chain A: K.9, S.11, A.156, K.157, N.158, V.160, G.162, V.163, Y.164, D.166, D.167, P.168, R.169, L.190, Q.191, V.192 Ligands: UDP.2, MG.7 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:A.156, A:N.158, A:N.158, A:Y.164, A:Y.164, A:R.169, A:R.169, A:Q.191 Water bridges: A:S.136 Salt bridges: A:K.9, A:K.157, A:K.157 ADP.8: 18 residues within 4Å: Chain B: K.9, S.11, D.138, A.156, K.157, N.158, V.160, G.162, V.163, Y.164, D.166, D.167, P.168, R.169, L.190, Q.191, V.192 Ligands: UDP.9 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.138, B:N.158, B:N.158, B:Y.164, B:Y.164, B:R.169, B:R.169, B:Q.191 Water bridges: B:K.9, B:K.9 Salt bridges: B:K.9 ADP.17: 19 residues within 4Å: Chain C: K.9, S.11, D.138, A.156, K.157, N.158, V.160, G.162, V.163, Y.164, D.166, D.167, P.168, R.169, L.190, Q.191, V.192 Ligands: UDP.18, MG.24 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:D.138, C:A.156, C:N.158, C:N.158, C:Y.164, C:Y.164, C:R.169, C:Q.191 Salt bridges: C:K.9, C:K.157, C:K.157 ADP.25: 18 residues within 4Å: Chain D: K.9, S.11, A.156, K.157, N.158, V.160, G.162, V.163, Y.164, D.166, D.167, P.168, R.169, L.190, Q.191, V.192 Ligands: UDP.26, MG.31 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:A.156, D:N.158, D:N.158, D:Y.164, D:Y.164, D:R.169, D:R.169, D:Q.191 Water bridges: D:S.136 Salt bridges: D:K.9, D:K.157, D:K.157 ADP.32: 18 residues within 4Å: Chain E: K.9, S.11, D.138, A.156, K.157, N.158, V.160, G.162, V.163, Y.164, D.166, D.167, P.168, R.169, L.190, Q.191, V.192 Ligands: UDP.33 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:D.138, E:N.158, E:N.158, E:Y.164, E:Y.164, E:R.169, E:R.169, E:Q.191 Water bridges: E:K.9, E:K.9 Salt bridges: E:K.9 ADP.41: 19 residues within 4Å: Chain F: K.9, S.11, D.138, A.156, K.157, N.158, V.160, G.162, V.163, Y.164, D.166, D.167, P.168, R.169, L.190, Q.191, V.192 Ligands: UDP.42, MG.48 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:D.138, F:A.156, F:N.158, F:N.158, F:Y.164, F:Y.164, F:R.169, F:Q.191 Salt bridges: F:K.9, F:K.157, F:K.157

6 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.2: 19 residues within 4Å: Chain A: K.9, S.11, G.12, G.49, A.50, G.51, D.69, G.72, M.73, T.76, G.129, T.130, N.132, P.133, F.135, S.136, T.137 Ligands: ADP.1, MG.7 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.137 Hydrogen bonds: A:L.10, A:G.12, A:E.13, A:A.50, A:G.51, A:D.69, A:T.130, A:N.132, A:F.135, A:T.137, A:T.137 Water bridges: A:S.136, A:S.136 Salt bridges: A:K.9 UDP.9: 19 residues within 4Å: Chain B: K.9, L.10, S.11, G.12, E.13, G.49, A.50, G.51, D.69, G.72, M.73, T.76, G.129, T.130, N.132, F.135, S.136, T.137 Ligands: ADP.8 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.12, B:E.13, B:A.50, B:G.51, B:D.69, B:D.69, B:T.130, B:N.132, B:T.137, B:T.137 Water bridges: B:K.9, B:D.138, B:D.138 Salt bridges: B:K.9 UDP.18: 20 residues within 4Å: Chain C: K.9, S.11, G.12, E.13, G.49, A.50, G.51, A.68, D.69, G.72, M.73, G.129, T.130, N.132, P.133, F.135, S.136, T.137 Ligands: ADP.17, MG.24 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:T.137 Hydrogen bonds: C:L.10, C:G.12, C:E.13, C:A.50, C:G.51, C:D.69, C:D.69, C:T.130, C:N.132, C:S.136, C:T.137 Water bridges: C:R.55, C:D.69, C:F.135 Salt bridges: C:K.9, C:K.9 UDP.26: 19 residues within 4Å: Chain D: K.9, S.11, G.12, G.49, A.50, G.51, D.69, G.72, M.73, T.76, G.129, T.130, N.132, P.133, F.135, S.136, T.137 Ligands: ADP.25, MG.31 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:T.137 Hydrogen bonds: D:L.10, D:G.12, D:E.13, D:A.50, D:G.51, D:D.69, D:T.130, D:N.132, D:F.135, D:T.137, D:T.137 Water bridges: D:S.136, D:S.136 Salt bridges: D:K.9 UDP.33: 19 residues within 4Å: Chain E: K.9, L.10, S.11, G.12, E.13, G.49, A.50, G.51, D.69, G.72, M.73, T.76, G.129, T.130, N.132, F.135, S.136, T.137 Ligands: ADP.32 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.12, E:E.13, E:A.50, E:G.51, E:D.69, E:D.69, E:T.130, E:N.132, E:T.137, E:T.137 Water bridges: E:K.9, E:D.138, E:D.138 Salt bridges: E:K.9 UDP.42: 20 residues within 4Å: Chain F: K.9, S.11, G.12, E.13, G.49, A.50, G.51, A.68, D.69, G.72, M.73, G.129, T.130, N.132, P.133, F.135, S.136, T.137 Ligands: ADP.41, MG.48 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:T.137 Hydrogen bonds: F:L.10, F:G.12, F:E.13, F:A.50, F:G.51, F:D.69, F:D.69, F:T.130, F:N.132, F:S.136, F:T.137 Water bridges: F:R.55, F:D.69, F:F.135 Salt bridges: F:K.9, F:K.9

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

GTP.3: 12 residues within 4Å: Chain A: R.95, T.103, A.106, E.107, R.113, H.117, K.120, R.122 Chain F: I.110, R.112, R.113 Ligands: GTP.43 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:E.107, A:R.113 Water bridges: A:R.113, A:R.113, F:R.112 Salt bridges: A:R.95, A:E.107, A:R.113, A:R.113, A:R.113, A:H.117, A:K.120, A:R.122, A:R.122, F:R.113 GTP.10: 12 residues within 4Å: Chain B: R.95, T.103, A.106, E.107, R.113, H.117, K.120, R.122 Chain D: I.110, R.112, R.113 Ligands: GTP.19 19 PLIP interactions: 5 interactions with chain D, 14 interactions with chain B Hydrogen bonds: D:R.112, B:R.95, B:E.107, B:E.107, B:R.113 Water bridges: D:R.111, D:R.113, D:R.113, B:Q.84, B:R.113 Salt bridges: D:R.113, B:R.95, B:E.107, B:R.113, B:R.113, B:R.113, B:K.120, B:R.122, B:R.122 GTP.19: 14 residues within 4Å: Chain B: I.110, R.112, R.113 Chain C: R.95, T.103, A.106, E.107, P.108, R.113, H.117, K.120, R.122 Ligands: GTP.10, GTP.27 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:E.107, C:E.107, B:R.112 Water bridges: C:E.107, C:R.113 Salt bridges: C:R.95, C:E.107, C:R.113, C:R.113, C:R.113, C:H.117, C:R.122, C:R.122, B:R.113 GTP.27: 12 residues within 4Å: Chain C: I.110, R.112, R.113 Chain D: R.95, T.103, A.106, E.107, R.113, H.117, K.120, R.122 Ligands: GTP.19 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.107, D:R.113 Water bridges: D:R.113, D:R.113, C:R.112 Salt bridges: D:R.95, D:E.107, D:R.113, D:R.113, D:R.113, D:H.117, D:K.120, D:R.122, D:R.122, C:R.113 GTP.34: 12 residues within 4Å: Chain A: I.110, R.112, R.113 Chain E: R.95, T.103, A.106, E.107, R.113, H.117, K.120, R.122 Ligands: GTP.43 19 PLIP interactions: 14 interactions with chain E, 5 interactions with chain A Hydrogen bonds: E:R.95, E:E.107, E:E.107, E:R.113, A:R.112 Water bridges: E:Q.84, E:R.113, A:R.111, A:R.113, A:R.113 Salt bridges: E:R.95, E:E.107, E:R.113, E:R.113, E:R.113, E:K.120, E:R.122, E:R.122, A:R.113 GTP.43: 14 residues within 4Å: Chain E: I.110, R.112, R.113 Chain F: R.95, T.103, A.106, E.107, P.108, R.113, H.117, K.120, R.122 Ligands: GTP.3, GTP.34 14 PLIP interactions: 12 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:E.107, F:E.107, E:R.112 Water bridges: F:E.107, F:R.113 Salt bridges: F:R.95, F:E.107, F:R.113, F:R.113, F:R.113, F:H.117, F:R.122, F:R.122, E:R.113

26 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: P.93, R.95, R.122 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: D.64, R.65 Ligand excluded by PLIP SO4.6: 1 residues within 4Å: Chain A: R.176 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain B: D.64, R.65 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: F.177, D.178, E.179 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: P.93, R.95, R.122 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: R.176, K.227, V.228, G.229 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: E.184, N.187, R.188 Ligand excluded by PLIP SO4.16: 1 residues within 4Å: Chain B: R.176 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain C: P.93, R.95, R.122 Ligand excluded by PLIP SO4.21: 1 residues within 4Å: Chain C: R.176 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain C: D.64, R.65 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain C: R.176, F.177, D.178, E.179 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain D: P.93, R.95, R.122 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain D: D.64, R.65 Ligand excluded by PLIP SO4.30: 1 residues within 4Å: Chain D: R.176 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain E: D.64, R.65 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain E: F.177, D.178, E.179 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain E: P.93, R.95, R.122 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain E: R.176, K.227, V.228, G.229 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain E: E.184, N.187, R.188 Ligand excluded by PLIP SO4.40: 1 residues within 4Å: Chain E: R.176 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain F: P.93, R.95, R.122 Ligand excluded by PLIP SO4.45: 1 residues within 4Å: Chain F: R.176 Ligand excluded by PLIP SO4.46: 2 residues within 4Å: Chain F: D.64, R.65 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain F: R.176, F.177, D.178, E.179 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 6 residues within 4Å: Chain A: K.9, S.136, D.138, K.157 Ligands: ADP.1, UDP.2 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain C: S.11 Ligands: ADP.17, UDP.18 No protein-ligand interaction detected (PLIP) MG.31: 6 residues within 4Å: Chain D: K.9, S.136, D.138, K.157 Ligands: ADP.25, UDP.26 No protein-ligand interaction detected (PLIP) MG.48: 3 residues within 4Å: Chain F: S.11 Ligands: ADP.41, UDP.42 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukui, K. et al., The crystal structure of Thermus thermophilus UMP kinase complexed with a phosphoryl group acceptor and donor. To Be Published

Release Date

2025-03-05

Peptides

Uridylate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Uridylate kinase

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