SMTL ID : 7xpu.1

crystal structure of MtdL-S228A-His soaked GDP-Fucp and Mn

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x GFB: GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE(Non-covalent)

GFB.1: 24 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, D.214, N.246, Q.248, F.262, R.276, D.279, H.306, R.308, N.309, H.311 Ligands: MN.2 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:T.32, A:I.34, A:N.61, A:N.61, A:R.109, A:D.128, A:D.128, A:D.128, A:D.129, A:D.129, A:D.130, A:R.178, A:Q.248, A:D.279, A:N.309 Water bridges: A:T.32, A:R.220, A:R.220, A:R.276, A:R.276, A:G.278 Salt bridges: A:D.59, A:R.178, A:R.276, A:R.276, A:H.306, A:R.308, A:H.311, A:H.311 GFB.3: 24 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, D.214, N.246, Q.248, F.262, R.276, D.279, H.306, R.308, N.309, H.311 Ligands: MN.5 28 PLIP interactions: 28 interactions with chain B Hydrogen bonds: B:T.32, B:T.33, B:I.34, B:N.61, B:R.109, B:D.128, B:D.129, B:D.129, B:D.130, B:R.178, B:Q.248, B:D.279, B:N.309 Water bridges: B:T.32, B:T.32, B:D.106, B:D.214, B:R.220, B:R.276, B:G.278 Salt bridges: B:D.59, B:R.178, B:R.276, B:R.276, B:H.306, B:R.308, B:H.311, B:H.311 GFB.6: 24 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, D.214, N.246, Q.248, F.262, R.276, D.279, H.306, R.308, N.309, H.311 Ligands: MN.7 30 PLIP interactions: 30 interactions with chain C Hydrogen bonds: C:T.32, C:T.33, C:I.34, C:N.61, C:N.61, C:R.109, C:D.128, C:D.128, C:D.128, C:D.129, C:D.129, C:D.130, C:R.178, C:Q.248, C:D.279, C:N.309 Water bridges: C:T.32, C:R.220, C:R.220, C:R.276, C:R.276, C:G.278 Salt bridges: C:D.59, C:R.178, C:R.276, C:R.276, C:H.306, C:R.308, C:H.311, C:H.311 GFB.8: 24 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, D.214, N.246, Q.248, F.262, R.276, D.279, H.306, R.308, N.309, H.311 Ligands: MN.10 28 PLIP interactions: 28 interactions with chain D Hydrogen bonds: D:T.32, D:I.34, D:N.61, D:R.109, D:D.128, D:D.128, D:D.129, D:D.129, D:D.130, D:R.178, D:Q.248, D:D.279, D:N.309 Water bridges: D:T.32, D:T.32, D:D.106, D:R.220, D:Q.248, D:R.276, D:G.278 Salt bridges: D:D.59, D:R.178, D:R.276, D:R.276, D:H.306, D:R.308, D:H.311, D:H.311

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

MN.2: 3 residues within 4Å: Chain A: D.130, H.306 Ligands: GFB.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.130, A:D.130, A:H.306, H2O.1 MN.5: 3 residues within 4Å: Chain B: D.130, H.306 Ligands: GFB.3 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.130, B:D.130, B:H.306, H2O.14 MN.7: 3 residues within 4Å: Chain C: D.130, H.306 Ligands: GFB.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.130, C:D.130, C:H.306, H2O.24 MN.10: 3 residues within 4Å: Chain D: D.130, H.306 Ligands: GFB.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.130, D:D.130, D:H.306, H2O.37

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain B: V.154, R.198, P.199, A.200, L.237, A.238, E.239, A.296 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.239 Water bridges: B:H.295, B:H.295 GOL.9: 8 residues within 4Å: Chain D: V.154, R.198, P.199, A.200, L.237, A.238, E.239, A.296 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.239 Water bridges: D:H.295, D:H.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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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