SMTL ID : 6yuq.1

Capsule O-acetyltransferase of Neisseria meningitidis serogroup A in complex with polysaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: T.68, Y.70, T.82, N.83 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.83, A:N.83 EDO.10: 4 residues within 4Å: Chain C: T.68, Y.70, T.82, N.83 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.83, C:N.83

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 6 residues within 4Å: Chain A: N.83, Y.155, M.156, G.158, N.167 Chain C: S.160 No protein-ligand interaction detected (PLIP) PEG.11: 6 residues within 4Å: Chain A: S.160 Chain C: N.83, Y.155, M.156, G.158, N.167 No protein-ligand interaction detected (PLIP)

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 7 residues within 4Å: Chain A: A.39, F.40, S.114, K.115, Y.144, R.148 Ligands: BMX.5 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain B: A.39, F.40, S.114, K.115, Y.144, R.148 Ligand excluded by PLIP CL.12: 7 residues within 4Å: Chain C: A.39, F.40, S.114, K.115, Y.144, R.148 Ligands: BMX.14 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain D: A.39, F.40, S.114, K.115, Y.144, R.148 Ligand excluded by PLIP

6 x BMX: 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose(Non-covalent)

BMX.4: 10 residues within 4Å: Chain A: A.39, F.40, P.41, P.42, N.50, K.53, N.230, I.233, R.237 Ligands: BMX.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.53, A:N.230, A:N.230 BMX.5: 13 residues within 4Å: Chain A: A.39, F.40, P.42, S.113, S.114, Y.144, R.148, H.228, D.229, I.233 Ligands: CL.3, BMX.4, BMX.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.233 Hydrogen bonds: A:S.114, A:S.114, A:R.148, A:R.148 BMX.6: 7 residues within 4Å: Chain A: P.41, P.42, K.43, R.76, R.148 Ligands: BMX.5, BM3.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.41, A:K.43 Salt bridges: A:R.76, A:R.148 BMX.13: 10 residues within 4Å: Chain C: A.39, F.40, P.41, P.42, N.50, K.53, N.230, I.233, R.237 Ligands: BMX.14 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.53, C:N.230, C:N.230 BMX.14: 13 residues within 4Å: Chain C: A.39, F.40, P.42, S.113, S.114, Y.144, R.148, H.228, D.229, I.233 Ligands: CL.12, BMX.13, BMX.15 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.233 Hydrogen bonds: C:S.114, C:S.114, C:Y.144, C:R.148, C:R.148 BMX.15: 7 residues within 4Å: Chain C: P.41, P.42, K.43, R.76, R.148 Ligands: BMX.14, BM3.16 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:P.41, C:K.43 Salt bridges: C:R.76, C:R.148

2 x BM3: 2-acetamido-2-deoxy-alpha-D-mannopyranose(Non-covalent)

BM3.7: 4 residues within 4Å: Chain A: T.147, R.148, S.149 Ligands: BMX.6 No protein-ligand interaction detected (PLIP) BM3.16: 4 residues within 4Å: Chain C: T.147, R.148, S.149 Ligands: BMX.15 No protein-ligand interaction detected (PLIP)

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 7 residues within 4Å: Chain B: N.83, E.84, L.85, Y.155, M.156, G.158, N.167 No protein-ligand interaction detected (PLIP) PGE.17: 7 residues within 4Å: Chain D: N.83, E.84, L.85, Y.155, M.156, G.158, N.167 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fiebig, T. et al., Structural and mechanistic basis of capsule O-acetylation in Neisseria meningitidis serogroup A. Nat Commun (2020)

Release Date

2020-08-19

Peptides

SacC: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

SacC

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