SMTL ID : 7xpv.1

crysteal structure of MtdL-S228A-His soaked with GDP-Fucf and Mn

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x GRJ: [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{S},3~{S},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[(1~{S})-1-oxidanylethyl]oxolan-2-yl] hydrogen phosphate(Non-covalent)

GRJ.1: 20 residues within 4Å: Chain A: T.32, T.33, I.34, D.59, N.61, H.104, S.105, D.106, R.109, D.128, D.129, D.130, R.178, R.276, D.279, H.306, R.308, N.309, H.311 Ligands: MN.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:T.32, A:T.33, A:I.34, A:N.61, A:R.109, A:D.128, A:D.128, A:D.129, A:D.129, A:R.178, A:R.178, A:R.276, A:R.276, A:D.279, A:N.309 Water bridges: A:D.128, A:D.214, A:D.214, A:G.278, A:D.279 Salt bridges: A:D.59, A:R.276, A:R.276, A:R.308, A:H.311, A:H.311 GRJ.3: 20 residues within 4Å: Chain B: T.32, T.33, I.34, D.59, N.61, H.104, S.105, D.106, R.109, D.128, D.129, D.130, R.178, R.276, D.279, H.306, R.308, N.309, H.311 Ligands: MN.4 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:T.32, B:I.34, B:N.61, B:N.61, B:R.109, B:D.128, B:D.128, B:D.129, B:D.129, B:R.178, B:R.276, B:R.276, B:D.279, B:N.309 Water bridges: B:T.32, B:D.106, B:G.278 Salt bridges: B:D.59, B:R.276, B:R.276, B:R.308, B:H.311, B:H.311 GRJ.5: 20 residues within 4Å: Chain C: T.32, T.33, I.34, D.59, N.61, H.104, S.105, D.106, R.109, D.128, D.129, D.130, R.178, R.276, D.279, H.306, R.308, N.309, H.311 Ligands: MN.6 24 PLIP interactions: 24 interactions with chain C Hydrogen bonds: C:T.32, C:I.34, C:N.61, C:R.109, C:D.128, C:D.128, C:D.129, C:D.129, C:R.178, C:R.178, C:R.276, C:R.276, C:D.279, C:N.309 Water bridges: C:D.128, C:D.214, C:G.278, C:D.279 Salt bridges: C:D.59, C:R.276, C:R.276, C:R.308, C:H.311, C:H.311 GRJ.7: 20 residues within 4Å: Chain D: T.32, T.33, I.34, D.59, N.61, H.104, S.105, D.106, R.109, D.128, D.129, D.130, R.178, R.276, D.279, H.306, R.308, N.309, H.311 Ligands: MN.8 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:T.32, D:T.32, D:T.33, D:I.34, D:N.61, D:N.61, D:R.109, D:D.128, D:D.128, D:D.129, D:D.129, D:R.178, D:R.276, D:R.276, D:D.279, D:N.309 Water bridges: D:T.32, D:D.106, D:G.278 Salt bridges: D:D.59, D:R.276, D:R.276, D:R.308, D:H.311, D:H.311

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

MN.2: 4 residues within 4Å: Chain A: D.130, H.306, R.308 Ligands: GRJ.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.130, A:D.130, A:H.306 MN.4: 4 residues within 4Å: Chain B: D.130, H.306, R.308 Ligands: GRJ.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.130, B:D.130, B:H.306 MN.6: 4 residues within 4Å: Chain C: D.130, H.306, R.308 Ligands: GRJ.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.130, C:D.130, C:H.306 MN.8: 4 residues within 4Å: Chain D: D.130, H.306, R.308 Ligands: GRJ.7 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.130, D:D.130, D:H.306

Links

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Citation

Du, X. et al., Structures of the NDP-pyranose mutase belonging to glycosyltransferase family 75 reveal residues important for Mn 2+ coordination and substrate binding. J.Biol.Chem. (2023)

Release Date

2023-03-29

Peptides

Transglycosylse: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Transglycosylse

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