SMTL ID : 3nwy.1

Structure and allosteric regulation of the uridine monophosphate kinase from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

homo-hexamer

Ligands

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

GTP.1: 14 residues within 4Å: Chain A: R.143, G.151, Q.152, A.154, E.155, P.156, R.161, H.165, K.168, R.170 Chain D: L.158, L.160, R.161, R.164 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.143, A:R.143, A:G.151, A:G.151, A:R.161 Salt bridges: A:R.143, A:R.161, A:R.161, A:H.165, A:K.168, A:K.168, A:R.170, A:R.170, D:R.161, D:R.164 GTP.2: 14 residues within 4Å: Chain B: R.143, G.151, Q.152, V.153, A.154, E.155, P.156, R.161, K.168, R.170 Chain C: L.158, L.160, R.161, R.164 18 PLIP interactions: 2 interactions with chain C, 16 interactions with chain B Hydrogen bonds: C:R.161, C:R.164, B:R.143, B:G.151, B:G.151, B:E.155 Water bridges: B:R.143, B:R.143, B:H.165, B:R.170 Salt bridges: B:R.143, B:R.143, B:R.161, B:R.161, B:K.168, B:K.168, B:R.170, B:R.170 GTP.4: 14 residues within 4Å: Chain C: R.143, G.151, Q.152, A.154, E.155, P.156, R.161, K.168, R.170 Chain E: L.158, L.160, R.161, R.164, K.168 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain E Hydrogen bonds: C:R.143, C:G.151, C:G.151, C:E.155, E:R.161, E:R.164 Salt bridges: C:R.143, C:R.161, C:R.161, C:K.168, C:K.168, C:R.170, C:R.170, E:R.161, E:K.168 GTP.5: 12 residues within 4Å: Chain D: R.143, G.151, Q.152, A.154, E.155, P.156, K.168, R.170 Chain F: L.158, L.160, R.161, R.164 10 PLIP interactions: 1 interactions with chain F, 9 interactions with chain D Salt bridges: F:R.161, D:R.143, D:K.168, D:K.168, D:R.170, D:R.170 Hydrogen bonds: D:R.143, D:R.143, D:G.151, D:G.151 GTP.6: 14 residues within 4Å: Chain B: L.158, L.160, R.161, R.164, K.168 Chain E: R.143, G.151, Q.152, V.153, A.154, E.155, P.156, K.168, R.170 12 PLIP interactions: 8 interactions with chain E, 4 interactions with chain B Hydrogen bonds: E:R.143, E:G.151, E:G.151, E:E.155 Salt bridges: E:R.143, E:R.143, E:K.168, E:R.170, B:R.161, B:R.164, B:K.168 Water bridges: B:R.170 GTP.7: 12 residues within 4Å: Chain A: L.160, R.161 Chain F: R.143, G.151, Q.152, V.153, A.154, E.155, P.156, R.161, K.168, R.170 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:R.143, F:R.143, F:G.151, F:G.151, F:R.161, A:R.161 Salt bridges: F:R.143, F:R.161, F:R.161, F:K.168, F:K.168, F:R.170, F:R.170

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

UDP.3: 22 residues within 4Å: Chain B: K.56, G.58, G.59, E.60, G.96, G.97, G.98, F.101, R.102, G.103, D.117, G.120, M.121, G.177, M.178, G.179, L.180, P.181, F.183, S.184, T.185, T.188 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.59, B:E.60, B:G.97, B:G.98, B:D.117, B:D.117, B:M.178, B:G.179, B:L.180, B:T.185, B:T.185 Water bridges: B:Y.182, B:S.184 Salt bridges: B:K.56, B:K.56, B:R.102, B:R.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Labesse, G. et al., Structural and functional characterization of the Mycobacterium tuberculosis uridine monophosphate kinase: insights into the allosteric regulation. Nucleic Acids Res. (2011)

Release Date

2010-08-25

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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