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

WbbB D232N-Kdo adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

C5P.1: 14 residues within 4Å: Chain A: P.162, R.164, V.227, L.228, Q.229, R.264, A.265, H.266, P.267, S.286, S.301, S.302, V.303 Ligands: KDO.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.227, A:V.303 Hydrogen bonds: A:P.162, A:L.228, A:R.264, A:R.264, A:S.286, A:S.286, A:S.302 Water bridges: A:Q.229, A:Q.229, A:H.266, A:S.286 Salt bridges: A:R.164, A:H.266 C5P.5: 14 residues within 4Å: Chain B: P.162, R.164, V.227, L.228, Q.229, R.264, A.265, H.266, P.267, S.286, S.301, S.302, V.303 Ligands: KDO.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:V.227, B:V.303 Hydrogen bonds: B:P.162, B:L.228, B:R.264, B:R.264, B:S.286, B:S.286, B:S.302 Water bridges: B:Q.229, B:Q.229, B:H.266, B:S.286 Salt bridges: B:R.164, B:H.266

2 x KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid(Post Translational Modification)

KDO.2: 11 residues within 4Å: Chain A: R.13, E.159, I.160, R.164, N.180, V.230, N.233, S.234, N.235, H.266 Ligands: C5P.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.164, A:R.164, A:N.180, A:N.180, A:S.234 Water bridges: A:R.13, A:S.234 Salt bridges: A:R.13 KDO.6: 11 residues within 4Å: Chain B: R.13, E.159, I.160, R.164, N.180, V.230, N.233, S.234, N.235, H.266 Ligands: C5P.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.164, B:R.164, B:N.180, B:N.180, B:N.233, B:S.234 Water bridges: B:Y.19, B:S.234 Salt bridges: B:R.13

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

NA.3: 4 residues within 4Å: Chain A: Y.173, N.180, C.320, S.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.173, A:S.321 NA.4: 3 residues within 4Å: Chain A: N.207, Y.208, L.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.208 NA.7: 4 residues within 4Å: Chain B: Y.173, N.180, C.320, S.321 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.173, B:S.321 NA.8: 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

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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