SMTL ID : 8cse.1 (1 other biounit)

WbbB in complex with alpha-Rha-(1-3)-beta-GlcNAc acceptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

6 x NAG- RAM: alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-RAM.1: 13 residues within 4Å: Chain A: R.13, P.18, Y.19, W.21, W.55, L.65, I.138, E.159, I.160, R.164, V.230, H.266, G.268 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.55, A:L.65, A:I.160, A:Y.19 Water bridges: A:R.13, A:R.164, A:S.234 Hydrogen bonds: A:R.13, A:R.13, A:W.21, A:E.159 NAG-RAM.2: 10 residues within 4Å: Chain A: K.25, H.28, C.29, A.63, S.64, L.65, G.66, N.170, F.349, D.350 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.25, A:N.170, A:D.350, A:D.350 Water bridges: A:N.170 NAG-RAM.3: 12 residues within 4Å: Chain A: Y.251, R.255, E.295, F.297, K.313, T.314, T.315, V.316, L.317, N.326 Chain B: H.97 Ligands: PXV.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.251, A:R.255, A:T.315, A:V.316, A:V.316, A:N.326 Water bridges: A:E.327 NAG-RAM.8: 13 residues within 4Å: Chain B: R.13, P.18, Y.19, W.21, W.55, L.65, I.138, E.159, I.160, R.164, V.230, H.266, G.268 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.55, B:L.65, B:I.160, B:Y.19 Water bridges: B:R.13, B:R.164, B:S.234 Hydrogen bonds: B:R.13, B:R.13, B:W.21, B:E.159 NAG-RAM.9: 10 residues within 4Å: Chain B: K.25, H.28, C.29, A.63, S.64, L.65, G.66, N.170, F.349, D.350 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.25, B:N.170, B:D.350, B:D.350 Water bridges: B:N.170 NAG-RAM.10: 12 residues within 4Å: Chain A: H.97 Chain B: Y.251, R.255, E.295, F.297, K.313, T.314, T.315, V.316, L.317, N.326 Ligands: PXV.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.251, B:R.255, B:T.315, B:V.316, B:V.316, B:N.326

2 x PXV: N-(8-hydroxyoctyl)-4-methoxybenzamide(Non-covalent)

PXV.4: 12 residues within 4Å: Chain A: R.253, Q.254, R.255 Chain B: P.11, G.14, L.15, K.16, Y.88, E.89, L.92, H.97 Ligands: NAG-RAM.3 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.254, A:R.255, A:R.255 Hydrophobic interactions: B:P.11, B:E.89 PXV.11: 12 residues within 4Å: Chain A: P.11, G.14, L.15, K.16, Y.88, E.89, L.92, H.97 Chain B: R.253, Q.254, R.255 Ligands: NAG-RAM.10 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.254, B:R.255, B:R.255 Hydrophobic interactions: A:P.11, A:E.89

2 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.5: 15 residues within 4Å: Chain A: P.162, R.164, V.227, L.228, Q.229, D.233, R.264, A.265, H.266, P.267, S.286, S.301, S.302, V.303, E.306 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.227, A:V.303 Hydrogen bonds: A:L.228, A:L.228, A:Q.229, A:D.233, A:R.264, A:S.286, A:S.286, A:S.302 Water bridges: A:P.162, A:V.230, A:H.266, A:S.286, A:N.300 Salt bridges: A:R.164, A:H.266 C5P.12: 15 residues within 4Å: Chain B: P.162, R.164, V.227, L.228, Q.229, D.233, R.264, A.265, H.266, P.267, S.286, S.301, S.302, V.303, E.306 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.227, B:V.303 Hydrogen bonds: B:L.228, B:L.228, B:Q.229, B:D.233, B:D.233, B:R.264, B:S.286, B:S.286, B:S.302 Water bridges: B:P.162, B:V.230, B:H.266, B:S.286, B:N.300 Salt bridges: B:R.164, B:H.266

4 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain A: N.207, Y.208, L.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.210 NA.7: 4 residues within 4Å: Chain A: I.325, N.326, L.328, T.334 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.326, A:L.328 NA.13: 3 residues within 4Å: Chain B: N.207, Y.208, L.210 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.207 NA.14: 4 residues within 4Å: Chain B: I.325, N.326, L.328, T.334 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.328, B:T.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Forrester, T.J.B. et al., The retaining beta-Kdo glycosyltransferase WbbB uses a double-displacement mechanism with an intermediate adduct rearrangement step. Nat Commun (2022)

Release Date

2022-11-09

Peptides

N-acetyl glucosaminyl transferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

N-acetyl glucosaminyl transferase

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