SMTL ID : 3ek5.1

Unique GTP-binding Pocket and Allostery of UMP Kinase from a Gram-Negative Phytopathogen Bacterium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-hexamer

Ligands

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

GTP.1: 14 residues within 4Å: Chain B: R.103, N.111, D.112, V.113, C.114, E.115, R.121, R.130 Chain C: I.118, R.120, R.121, R.124, K.128 Ligands: GTP.3 19 PLIP interactions: 5 interactions with chain C, 14 interactions with chain B Hydrogen bonds: C:R.120, B:R.103, B:R.103, B:N.111, B:D.112, B:E.115, B:R.121 Salt bridges: C:R.121, C:R.124, C:K.128, C:K.128, B:R.103, B:R.103, B:R.121, B:K.128, B:R.130, B:R.130 Water bridges: B:R.103, B:R.103 GTP.2: 13 residues within 4Å: Chain C: R.103, N.111, D.112, V.113, C.114, E.115, R.121, R.130 Chain F: I.118, R.120, R.121, R.124, K.128 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain F Hydrogen bonds: C:R.103, C:N.111, C:N.111, F:R.120 Water bridges: C:D.112, C:R.130, F:R.120 Salt bridges: C:R.103, C:R.103, C:R.103, C:R.121, C:R.130, C:R.130, F:R.121, F:R.124, F:K.128, F:K.128 GTP.3: 14 residues within 4Å: Chain B: I.118, R.120, R.121, R.124, K.128 Chain F: R.103, N.111, D.112, V.113, C.114, E.115, R.121, R.130 Ligands: GTP.1 16 PLIP interactions: 10 interactions with chain F, 6 interactions with chain B Hydrogen bonds: F:R.103, F:R.103, F:N.111, F:N.111, F:E.115, F:R.130, F:R.130, B:R.120, B:R.121 Salt bridges: F:R.103, F:R.121, F:R.130, B:R.121, B:R.124, B:K.128, B:K.128 GTP.4: 15 residues within 4Å: Chain A: K.101, R.103, N.111, D.112, V.113, C.114, E.115, R.121, K.128, R.130 Chain E: I.118, R.120, R.121, R.124, K.128 18 PLIP interactions: 5 interactions with chain E, 13 interactions with chain A Hydrogen bonds: E:R.120, A:R.103, A:R.103, A:N.111, A:D.112, A:E.115 Salt bridges: E:R.121, E:R.124, E:K.128, E:K.128, A:K.101, A:R.103, A:R.103, A:R.103, A:R.121, A:K.128, A:R.130, A:R.130 GTP.5: 15 residues within 4Å: Chain A: I.118, R.120, R.121, R.124, K.128 Chain D: R.103, N.111, D.112, V.113, C.114, E.115, R.121, K.128, R.130 Ligands: GTP.6 15 PLIP interactions: 9 interactions with chain D, 6 interactions with chain A Hydrogen bonds: D:R.103, D:N.111, D:D.112, A:R.120 Salt bridges: D:R.103, D:R.103, D:R.121, D:K.128, D:R.130, D:R.130, A:R.121, A:R.124, A:K.128, A:K.128 Water bridges: A:R.120 GTP.6: 16 residues within 4Å: Chain D: I.118, R.120, R.121, R.124, K.128 Chain E: K.101, R.103, N.111, D.112, V.113, C.114, E.115, R.121, K.128, R.130 Ligands: GTP.5 18 PLIP interactions: 5 interactions with chain D, 13 interactions with chain E Hydrogen bonds: D:R.120, E:R.103, E:N.111, E:N.111, E:R.121 Salt bridges: D:R.121, D:R.124, D:K.128, D:K.128, E:K.101, E:R.103, E:R.103, E:R.103, E:R.121, E:K.128, E:K.128, E:R.130, E:R.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tu, J.-L. et al., Unique GTP-Binding Pocket and Allostery of Uridylate Kinase from a Gram-Negative Phytopathogenic Bacterium. J.Mol.Biol. (2009)

Release Date

2008-12-23

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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