SMTL ID : 7bl7.2 (1 other biounit)

Crystal structure of UMPK from M. tuberculosis in complex with UDP and UTP (P21212 form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.33 Å

Oligo State

homo-hexamer

Ligands

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

UTP.1: 15 residues within 4Å: Chain A: R.143, V.144, G.151, A.154, E.155, R.161, H.165, K.168, R.170 Chain C: L.158, L.160, R.161, R.164, K.168 Ligands: UTP.7 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:E.155 Hydrogen bonds: A:V.144, A:G.151, A:E.155, A:E.155 Salt bridges: A:R.143, A:R.161, A:R.161, A:H.165, A:K.168, A:R.170, A:R.170, C:R.164, C:R.164, C:K.168, C:K.168 UTP.3: 16 residues within 4Å: Chain B: R.143, G.151, A.154, E.155, P.156, R.161, H.165, K.168, R.170 Chain D: R.161 Chain F: L.158, L.160, R.161, R.164, K.168 Ligands: UTP.6 22 PLIP interactions: 6 interactions with chain F, 15 interactions with chain B, 1 interactions with chain D Salt bridges: F:R.161, F:R.164, F:R.164, F:K.168, F:K.168, F:K.168, B:R.143, B:R.161, B:R.161, B:R.161, B:H.165, B:K.168, B:R.170, B:R.170 Hydrophobic interactions: B:E.155 Hydrogen bonds: B:R.143, B:V.144, B:G.151, B:E.155, D:R.161 Water bridges: B:V.144, B:V.144 UTP.6: 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.3 14 PLIP interactions: 6 interactions with chain B, 8 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:R.170, D:R.170 Hydrogen bonds: D:G.151 UTP.7: 15 residues within 4Å: Chain A: L.158, L.160, R.161, R.164, K.168 Chain E: R.143, G.151, A.154, E.155, P.156, R.161, H.165, K.168, R.170 Ligands: UTP.1 19 PLIP interactions: 12 interactions with chain E, 7 interactions with chain A Hydrophobic interactions: E:E.155, A:R.161 Hydrogen bonds: E:G.151, E:E.155 Water bridges: E:H.165 Salt bridges: E:R.143, E:R.161, E:R.161, E:R.161, E:H.165, E:K.168, E:R.170, E:R.170, A:R.161, A:R.164, A:R.164, A:K.168, A:K.168, A:K.168

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

UDP.2: 24 residues within 4Å: Chain A: K.56, G.58, G.59, G.96, G.97, G.98, F.101, R.102, G.103, A.104, D.117, G.120, M.121, T.124, G.177, M.178, G.179, L.180, P.181, Y.182, 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:Y.182, A:F.183, A:T.185 Salt bridges: A:K.56, A:R.102 UDP.4: 24 residues within 4Å: Chain B: K.56, G.58, G.59, G.96, G.97, G.98, F.101, R.102, G.103, S.116, D.117, G.120, M.121, T.124, G.177, M.178, G.179, L.180, P.181, F.183, S.184, T.185, D.186, T.188 13 PLIP interactions: 13 interactions with chain B 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:L.180, B:T.185 Salt bridges: B:K.56, B:K.56, B:R.102 UDP.5: 24 residues within 4Å: Chain C: K.56, G.58, G.59, G.96, G.97, G.98, F.101, R.102, G.103, S.116, D.117, G.120, M.121, T.124, G.177, M.178, G.179, L.180, P.181, Y.182, F.183, S.184, T.185, T.188 14 PLIP interactions: 14 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:T.185, C:T.185 Salt bridges: C:K.56, C:R.102 UDP.8: 24 residues within 4Å: Chain F: K.56, G.58, G.59, G.96, G.97, G.98, F.101, R.102, G.103, A.104, D.117, G.120, M.121, T.124, G.177, M.178, L.180, P.181, Y.182, F.183, S.184, T.185, D.186, T.188 14 PLIP interactions: 14 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:L.180, F:Y.182, F:F.183, F:T.185, F:T.185 Salt bridges: F:K.56, F:K.56, F:R.102

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

2022-03-02

Peptides

Uridylate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
L

E
G

F
H

Uridylate kinase

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