- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NAG- RAM: alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)
- 2 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)
C5P.2: 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.5
16 PLIP interactions:16 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.286, A:S.302
- Water bridges: A:Q.229, A:Q.229, A:Q.229, A:V.230
- Salt bridges: A:R.164, A:H.266
C5P.7: 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.10
16 PLIP interactions:16 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.286, B:S.302
- Water bridges: B:Q.229, B:Q.229, B:Q.229, B:V.230
- Salt bridges: B:R.164, B:H.266
- 4 x NA: SODIUM ION(Non-functional Binders)
NA.3: 4 residues within 4Å:- Chain A: H.119, H.146, V.147, T.150
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:H.146, A:T.150
NA.4: 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:L.328, A:T.334
NA.8: 4 residues within 4Å:- Chain B: H.119, H.146, V.147, T.150
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:H.119, B:H.146
NA.9: 4 residues within 4Å:- Chain B: I.325, N.326, L.328, T.334
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:T.334
- 2 x KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid(Post Translational Modification)
KDO.5: 13 residues within 4Å:- Chain A: R.13, E.159, I.160, R.164, N.180, V.230, C.233, S.234, N.235, H.266
- Ligands: NAG-RAM.1, NAG-RAM.1, C5P.2
12 PLIP interactions:12 interactions with chain A- Hydrogen bonds: A:R.164, A:R.164, A:N.180, A:N.180, A:S.234, A:S.234, A:N.235
- Water bridges: A:R.13, A:S.234, A:S.234, A:S.234
- Salt bridges: A:R.13
KDO.10: 13 residues within 4Å:- Chain B: R.13, E.159, I.160, R.164, N.180, V.230, C.233, S.234, N.235, H.266
- Ligands: NAG-RAM.6, NAG-RAM.6, C5P.7
12 PLIP interactions:12 interactions with chain B- Hydrogen bonds: B:R.164, B:R.164, B:N.180, B:N.180, B:S.234, B:S.234, B:N.235
- Water bridges: B:R.13, B:S.234, B:S.234, B:S.234
- Salt bridges: B:R.13
- 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
BB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NAG- RAM: alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)
- 2 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)
- 4 x NA: SODIUM ION(Non-functional Binders)
- 2 x KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid(Post Translational Modification)
- 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
BB
B