SMTL ID : 6ncs.1

Crystal structure of N-acetylneuraminic acid (Sialic acid) synthetase from Leptospira borgpetersenii serovar Hardjo-bovis in complex with citrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 3 residues within 4Å: Chain A: H.210, H.231 Ligands: CIT.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.210, A:H.231, H2O.1 MN.16: 3 residues within 4Å: Chain B: H.210, H.231 Ligands: CIT.17 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.210, B:H.231, H2O.11

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 12 residues within 4Å: Chain A: E.31, K.59, Q.61, T.106, K.125, A.127, S.128, Y.182, H.210, E.229, H.231 Ligands: MN.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.127 Hydrogen bonds: A:Q.61, A:T.106, A:S.128 Water bridges: A:K.125, A:S.128, A:Y.182, A:S.208, A:S.208 Salt bridges: A:K.59, A:K.125, A:K.125, A:H.210, A:H.210, A:H.231 CIT.17: 12 residues within 4Å: Chain B: E.31, K.59, Q.61, T.106, F.108, K.125, A.127, S.128, Y.182, H.210, H.231 Ligands: MN.16 19 PLIP interactions: 1 interactions with chain A, 18 interactions with chain B Water bridges: A:E.280, B:R.68, B:K.125, B:S.128, B:S.128, B:C.129, B:S.150 Hydrophobic interactions: B:F.108, B:A.127 Hydrogen bonds: B:E.31, B:Q.61, B:S.128, B:Y.182 Salt bridges: B:K.59, B:K.125, B:K.125, B:H.210, B:H.210, B:H.231

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: E.12, I.13, T.14, P.172 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.172 Hydrogen bonds: A:E.12, A:T.14, A:T.14

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 2 residues within 4Å: Chain A: S.199, K.200 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.199

1 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.5: 8 residues within 4Å: Chain A: E.215, L.218, R.261, I.262 Chain B: E.215, L.218, R.261, I.262 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.215, B:R.261, A:E.215, A:R.261 Water bridges: B:E.258, A:E.258

20 x IOD: IODIDE ION(Non-functional Binders)

IOD.6: 1 residues within 4Å: Chain A: R.45 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: Q.97, L.102, F.103 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: K.86, M.115, E.118 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: N.185, I.187 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: G.213, I.214, A.247, E.251 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: L.271 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain A: K.250 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: K.98, K.99 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain A: E.202 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain A: I.245 Ligand excluded by PLIP IOD.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain B: Q.97, F.103 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain B: K.86, M.115 Ligand excluded by PLIP IOD.21: 1 residues within 4Å: Chain B: E.202 Ligand excluded by PLIP IOD.22: 2 residues within 4Å: Chain B: K.270, L.271 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain B: L.42, R.45 Ligand excluded by PLIP IOD.24: 3 residues within 4Å: Chain B: Y.182, D.242, I.245 Ligand excluded by PLIP IOD.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.26: 1 residues within 4Å: Chain B: I.214 Ligand excluded by PLIP IOD.27: 1 residues within 4Å: Chain B: K.212 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of N-acetylneuraminic acid (Sialic acid) synthetase from Leptospira borgpetersenii serovar Hardjo-bovis in complex with citrate. to be published

Release Date

2018-12-26

Peptides

N-acetylneuraminic acid (Sialic acid) synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-acetylneuraminic acid (Sialic acid) synthetase