SMTL ID : 7bes.1

CryoEM structure of Mycobacterium tuberculosis UMP Kinase (UMPK) in complex with UDP and UTP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

UDP.1: 20 residues within 4Å: Chain A: K.56, G.58, G.59, 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 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.59, A:G.97, A:G.98, A:G.103, A:D.117, A:D.117, A:M.178, A:G.179, A:L.180, A:L.180, A:F.183, A:T.185 Salt bridges: A:K.56, A:R.102 UDP.2: 20 residues within 4Å: Chain B: K.56, G.58, G.59, G.96, G.97, G.98, F.101, R.102, G.103, D.117, G.120, M.121, G.177, M.178, L.180, P.181, F.183, S.184, T.185, T.188 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:T.185 Hydrogen bonds: B:G.59, B:G.97, B:G.98, B:G.103, B:D.117, B:M.178, B:G.179, B:L.180, B:Y.182, B:F.183, B:T.185, B:T.185, B:T.185, B:T.188 Salt bridges: B:K.56, B:R.102 UDP.4: 20 residues within 4Å: Chain C: K.56, G.58, G.59, G.96, G.97, G.98, F.101, R.102, G.103, D.117, G.120, G.177, M.178, G.179, L.180, P.181, Y.182, F.183, T.185, T.188 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:G.59, C:G.97, C:G.98, C:G.103, C:D.117, C:M.178, C:G.179, C:L.180, C:Y.182, C:F.183, C:F.183, C:T.185, C:T.185 Salt bridges: C:K.56, C:R.102 UDP.6: 20 residues within 4Å: Chain D: K.56, G.58, G.59, 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 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.59, D:G.97, D:G.98, D:G.103, D:D.117, D:D.117, D:M.178, D:G.179, D:L.180, D:L.180, D:F.183, D:T.185 Salt bridges: D:K.56, D:R.102 UDP.7: 20 residues within 4Å: Chain E: K.56, G.58, G.59, G.96, G.97, G.98, F.101, R.102, G.103, D.117, G.120, M.121, G.177, M.178, L.180, P.181, F.183, S.184, T.185, T.188 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:T.185 Hydrogen bonds: E:G.59, E:G.97, E:G.98, E:G.103, E:D.117, E:M.178, E:G.179, E:L.180, E:Y.182, E:F.183, E:T.185, E:T.185, E:T.185, E:T.188 Salt bridges: E:K.56, E:R.102 UDP.9: 20 residues within 4Å: Chain F: K.56, G.58, G.59, G.96, G.97, G.98, F.101, R.102, G.103, D.117, G.120, G.177, M.178, G.179, L.180, P.181, Y.182, F.183, T.185, T.188 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:G.59, F:G.97, F:G.98, F:G.103, F:D.117, F:M.178, F:G.179, F:L.180, F:Y.182, F:F.183, F:F.183, F:T.185, F:T.185 Salt bridges: F:K.56, F:R.102

4 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.3: 15 residues within 4Å: Chain B: L.158, L.160, R.161, R.164, K.168 Chain D: R.143, G.151, A.154, E.155, P.156, R.161, H.165, K.168, R.170 Ligands: UTP.10 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain D Salt bridges: B:R.161, B:R.164, B:R.164, B:K.168, B:K.168, B:K.168, D:R.143, D:R.161, D:R.161, D:R.161, D:H.165, D:K.168, D:R.170, D:R.170 Hydrophobic interactions: D:E.155 Hydrogen bonds: D:G.151 UTP.5: 16 residues within 4Å: Chain A: L.158, L.160, R.161, R.164, K.168 Chain C: R.143, G.151, A.154, E.155, P.156, R.161, R.164, H.165, K.168, R.170 Ligands: UTP.8 18 PLIP interactions: 11 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:E.155, A:R.161 Hydrogen bonds: C:G.151, C:R.164 Salt bridges: C:R.143, C:R.161, C:R.161, C:R.161, C:H.165, C:K.168, C:R.170, C:R.170, A:R.161, A:R.164, A:R.164, A:K.168, A:K.168, A:K.168 UTP.8: 15 residues within 4Å: Chain A: R.143, G.151, A.154, E.155, P.156, R.161, H.165, K.168, R.170 Chain E: L.158, L.160, R.161, R.164, K.168 Ligands: UTP.5 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain E Hydrophobic interactions: A:E.155 Hydrogen bonds: A:G.151 Salt bridges: A:R.143, A:R.161, A:R.161, A:R.161, A:H.165, A:K.168, A:R.170, A:R.170, E:R.161, E:R.164, E:R.164, E:K.168, E:K.168, E:K.168 UTP.10: 16 residues within 4Å: Chain D: L.158, L.160, R.161, R.164, K.168 Chain F: R.143, G.151, A.154, E.155, P.156, R.161, R.164, H.165, K.168, R.170 Ligands: UTP.3 18 PLIP interactions: 11 interactions with chain F, 7 interactions with chain D Hydrophobic interactions: F:E.155, D:R.161 Hydrogen bonds: F:G.151, F:R.164 Salt bridges: F:R.143, F:R.161, F:R.161, F:R.161, F:H.165, F:K.168, F:R.170, F:R.170, D:R.161, D:R.164, D:R.164, D:K.168, D:K.168, D:K.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walter, P. et al., Structural basis for the allosteric inhibition of UMP kinase from Gram-positive bacteria, a promising antibacterial target. Febs J. (2022)

Release Date

2022-01-12

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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