SMTL ID : 6rb7.1

Ruminococcus gnavus sialic acid aldolase catalytic lysine mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 9 residues within 4Å: Chain A: G.223, P.224, D.225, E.226, G.242, T.243, M.287, Y.288 Ligands: GOL.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.225, A:D.225, A:G.242, A:Y.288 Water bridges: A:S.81, A:S.200, A:D.225, A:Y.288 TRS.8: 9 residues within 4Å: Chain B: G.223, P.224, D.225, E.226, G.242, T.243, M.287, Y.288 Ligands: GOL.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.225, B:D.225, B:G.242, B:Y.288 Water bridges: B:S.81, B:S.200, B:D.225, B:E.226, B:E.226, B:Y.288 TRS.11: 8 residues within 4Å: Chain C: G.223, P.224, D.225, E.226, G.242, T.243, M.287, Y.288 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.225, C:D.225, C:G.242, C:Y.288, C:Y.288 Water bridges: C:G.223, C:D.225, C:E.226, C:E.226 TRS.14: 9 residues within 4Å: Chain D: G.223, P.224, D.225, E.226, G.242, T.243, M.287, Y.288 Ligands: GOL.15 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:D.225, D:D.225, D:G.242, D:Y.288, D:Y.288 Water bridges: D:S.81, D:G.223, D:E.226, D:Y.288

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: C.281, N.286, M.287, Y.288 Chain B: F.144 Ligands: TRS.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.286 Water bridges: A:M.287 GOL.4: 3 residues within 4Å: Chain A: E.97, M.100, K.101 No protein-ligand interaction detected (PLIP) GOL.6: 7 residues within 4Å: Chain A: H.145, P.173, Q.174, G.177 Chain B: H.145, Q.174, G.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.174 GOL.9: 6 residues within 4Å: Chain A: F.144 Chain B: C.281, N.286, M.287, Y.288 Ligands: TRS.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.286 Water bridges: B:M.287, B:Y.288, B:Y.288 GOL.12: 4 residues within 4Å: Chain C: N.286, Y.288 Chain D: F.144 Ligands: MG.13 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.286 Water bridges: C:M.287, D:H.145 GOL.15: 4 residues within 4Å: Chain C: F.144 Chain D: N.286, Y.288 Ligands: TRS.14 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.286 Water bridges: D:M.287

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

PEG.3: 5 residues within 4Å: Chain A: R.267, Y.271 Chain C: K.211, G.235, E.237 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.267 PEG.16: 3 residues within 4Å: Chain D: E.104, G.105, K.106 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.106 Water bridges: D:K.106 PEG.17: 5 residues within 4Å: Chain B: K.211, G.235, E.237 Chain D: R.267, Y.271 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Water bridges: D:R.267 Hydrogen bonds: B:G.235

1 x BCN: BICINE(Non-covalent)

BCN.5: 5 residues within 4Å: Chain A: A.260, G.261, K.262 Chain C: A.260, G.261 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.263

4 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: N.286, P.311 Chain B: P.147 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain A: P.147 Chain B: N.286, P.311 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain C: N.286, P.311 Chain D: P.147 Ligands: GOL.12 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain C: P.147 Chain D: N.286, P.311 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bell, A. et al., Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut. Nat Microbiol (2019)

Release Date

2019-09-25

Peptides

Putative N-acetylneuraminate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

Putative N-acetylneuraminate lyase

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