SMTL ID : 9asc.1

Cryo-EM Structure of the Glycosyltransferase ArnC from Salmonella enterica in the UDP-bound State Determined on Talos Arctica microscope

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

UDP.1: 18 residues within 4Å: Chain A: P.51, V.52, Y.53, E.55, D.84, N.113, G.115, Q.116, D.136, A.137, D.138, Q.140, R.241, S.246, K.247, Y.248, R.252 Ligands: MN.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:P.51, A:P.51, A:Y.53, A:D.84, A:N.113, A:A.137, A:D.138, A:S.246, A:S.246, A:K.247, A:Y.248, A:R.252 Salt bridges: A:R.241 UDP.3: 18 residues within 4Å: Chain B: P.51, V.52, Y.53, E.55, D.84, N.113, G.115, Q.116, D.136, A.137, D.138, Q.140, R.241, S.246, K.247, Y.248, R.252 Ligands: MN.4 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:P.51, B:P.51, B:Y.53, B:D.84, B:N.113, B:A.137, B:D.138, B:S.246, B:S.246, B:K.247, B:Y.248, B:R.252 Salt bridges: B:R.241 UDP.5: 18 residues within 4Å: Chain C: P.51, V.52, Y.53, E.55, D.84, N.113, G.115, Q.116, D.136, A.137, D.138, Q.140, R.241, S.246, K.247, Y.248, R.252 Ligands: MN.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:P.51, C:P.51, C:Y.53, C:D.84, C:N.113, C:A.137, C:D.138, C:S.246, C:S.246, C:K.247, C:Y.248, C:R.252 Salt bridges: C:R.241 UDP.7: 18 residues within 4Å: Chain D: P.51, V.52, Y.53, E.55, D.84, N.113, G.115, Q.116, D.136, A.137, D.138, Q.140, R.241, S.246, K.247, Y.248, R.252 Ligands: MN.8 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:P.51, D:P.51, D:Y.53, D:D.84, D:N.113, D:A.137, D:D.138, D:S.246, D:S.246, D:K.247, D:Y.248, D:R.252 Salt bridges: D:R.241

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: D.138, Q.140, R.241, S.246 Ligands: UDP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.138 MN.4: 5 residues within 4Å: Chain B: D.138, Q.140, R.241, S.246 Ligands: UDP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.138 MN.6: 5 residues within 4Å: Chain C: D.138, Q.140, R.241, S.246 Ligands: UDP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.138 MN.8: 5 residues within 4Å: Chain D: D.138, Q.140, R.241, S.246 Ligands: UDP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ashraf, K.U. et al., Structural basis of undecaprenyl phosphate glycosylation leading to polymyxin resistance in Gram-negative bacteria. Biorxiv (2025)

Release Date

2025-02-05

Peptides

Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase

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