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

WbbB D232N in complex with CMP-beta-Kdo

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: R.13, Y.19, E.159, N.233, S.234 Ligands: CMK.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.19, A:N.233, A:S.234, A:S.234 Water bridges: A:S.234 Salt bridges: A:R.13 PO4.2: 2 residues within 4Å: Chain A: S.93, H.97 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.97 PO4.3: 4 residues within 4Å: Chain A: R.169, E.211, F.377, Y.378 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.211 Salt bridges: A:R.169 PO4.6: 6 residues within 4Å: Chain B: R.13, Y.19, E.159, N.233, S.234 Ligands: CMK.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.233, B:S.234, B:S.234 Water bridges: B:S.234 Salt bridges: B:R.13 PO4.7: 2 residues within 4Å: Chain B: S.93, H.97 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.97 PO4.8: 4 residues within 4Å: Chain B: R.169, E.211, F.377, Y.378 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.211 Salt bridges: B:R.169

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

C5P.4: 15 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, E.306 Ligands: CMK.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.303 Hydrogen bonds: A:L.228, A:R.264, A:R.264, A:S.286, A:S.302 Salt bridges: A:R.164, A:H.266 C5P.9: 15 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, E.306 Ligands: CMK.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.303 Hydrogen bonds: B:L.228, B:R.264, B:R.264, B:S.286, B:S.302 Salt bridges: B:R.164, B:H.266

2 x CMK: CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID(Non-covalent)

CMK.5: 23 residues within 4Å: Chain A: E.159, I.160, P.162, R.164, N.180, V.227, L.228, Q.229, V.230, N.233, S.234, N.235, R.264, A.265, H.266, P.267, S.286, S.301, S.302, V.303, E.306 Ligands: PO4.1, C5P.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.303 Hydrogen bonds: A:E.159, A:R.164, A:R.164, A:N.180, A:L.228, A:Q.229, A:V.230, A:N.233, A:N.235, A:R.264, A:R.264, A:H.266, A:S.286, A:S.301, A:S.302 Salt bridges: A:R.164, A:H.266, A:H.266 CMK.10: 23 residues within 4Å: Chain B: E.159, I.160, P.162, R.164, N.180, V.227, L.228, Q.229, V.230, N.233, S.234, N.235, R.264, A.265, H.266, P.267, S.286, S.301, S.302, V.303, E.306 Ligands: PO4.6, C5P.9 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.303 Hydrogen bonds: B:R.164, B:R.164, B:N.180, B:L.228, B:Q.229, B:V.230, B:N.233, B:N.235, B:R.264, B:R.264, B:H.266, B:S.286, B:S.301, B:S.302 Salt bridges: B:R.164, B:H.266, B:H.266

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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