SMTL ID : 2wlg.1

CRYSTALLOGRAPHIC ANALYSIS OF THE POLYSIALIC ACID O-ACETYLTRANSFERASE OATWY

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

2 x SOP: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-2,2-DIMETHYL-4-OXO-4-{[3-OXO-3-({2-[(2-OXOPROPYL)THIO]ETHYL}AMINO)PROPYL]AMINO}BUTYL DIHYDROGEN DIPHOSPHATE(Non-covalent)

SOP.1: 27 residues within 4Å: Chain A: R.116, D.119, H.121, I.123, N.133, K.154, Y.171, K.172, S.184, P.185 Chain C: M.108, A.110, W.145, L.146, G.147, R.148, V.163, G.165, S.166, V.180, A.182, G.183, V.189, K.190 Ligands: EDO.3, EDO.5, ACT.14 21 PLIP interactions: 12 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:I.123, C:A.110, C:V.163, C:V.180 Hydrogen bonds: A:D.119, A:D.119, C:R.148, C:S.166 Water bridges: A:K.154, A:K.154, A:K.154, A:K.154, C:G.183, C:G.183 Salt bridges: A:K.154, A:K.154, A:K.172, C:K.190, C:K.190 pi-Stacking: A:Y.171, A:Y.171 SOP.13: 24 residues within 4Å: Chain B: M.108, A.110, W.145, G.147, R.148, V.163, G.165, S.166, V.180, G.183, V.189, K.190 Chain C: R.116, D.119, H.121, I.123, I.132, N.133, L.153, K.154, Y.171 Ligands: ACT.10, EDO.16, EDO.18 21 PLIP interactions: 12 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: C:I.123, B:V.163, B:V.180 Hydrogen bonds: C:D.119, C:D.119, B:W.145, B:R.148, B:S.166, B:G.183 Water bridges: C:K.154, C:K.154, C:K.154, C:K.154, C:S.184, B:S.166 Salt bridges: C:K.154, C:K.154, B:K.190, B:K.190 pi-Stacking: C:Y.171, C:Y.171

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

EDO.2: 6 residues within 4Å: Chain A: N.34, N.35, S.36, N.56, I.57, T.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.36 EDO.3: 3 residues within 4Å: Chain A: M.120, H.121 Ligands: SOP.1 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: T.14, N.16, S.36, V.37, Y.38 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.16, A:V.37, A:V.37 Water bridges: A:S.36 EDO.5: 7 residues within 4Å: Chain A: V.169, S.184 Chain C: S.166, H.167, G.183, S.184 Ligands: SOP.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.167, C:S.184 Water bridges: C:G.183 EDO.6: 4 residues within 4Å: Chain A: G.147, V.163, G.165, S.166 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:R.116, B:Y.171 Hydrogen bonds: A:S.166 EDO.7: 4 residues within 4Å: Chain A: Y.6, N.13, T.14, I.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.15, A:I.15 EDO.8: 5 residues within 4Å: Chain A: H.75, A.96, E.97 Chain C: M.199 Ligands: ACT.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.97 Water bridges: A:K.98 EDO.9: 7 residues within 4Å: Chain A: K.136, K.154, G.155, V.156, Y.171, K.172, S.173 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.171, A:S.173 Water bridges: A:K.136 EDO.11: 4 residues within 4Å: Chain A: M.199 Chain B: H.75, A.96, E.97 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.97 Water bridges: B:K.98 EDO.12: 5 residues within 4Å: Chain B: D.119, I.123, I.132, N.133, K.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.119, B:K.154 EDO.16: 6 residues within 4Å: Chain B: R.148 Chain C: T.94, R.116, M.120 Ligands: ACT.10, SOP.13 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.94, C:T.94, C:R.116, C:R.116, B:R.148 EDO.17: 5 residues within 4Å: Chain C: L.170, Y.171, K.172, F.174, A.186 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.171, C:Y.171, C:K.172, C:K.172 EDO.18: 5 residues within 4Å: Chain B: G.183, S.184 Chain C: S.184, P.185 Ligands: SOP.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.184

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

ACT.10: 5 residues within 4Å: Chain B: A.110, H.111, R.148 Ligands: SOP.13, EDO.16 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.110, B:H.111 Hydrogen bonds: B:H.111 Salt bridges: B:H.111, B:R.148 ACT.14: 4 residues within 4Å: Chain C: A.110, H.111, R.148 Ligands: SOP.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.111 Salt bridges: C:H.111, C:R.148 ACT.15: 5 residues within 4Å: Chain C: R.197, K.198, M.199, Y.200 Ligands: EDO.8 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:M.199, C:Y.200 Water bridges: A:M.120, A:H.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, H.J. et al., Structural and Kinetic Characterizations of the Polysialic Acid O-Acetyltransferase Oatwy from Neisseria Meningitidis. J.Biol.Chem. (2009)

Release Date

2009-06-30

Peptides

POLYSIALIC ACID O-ACETYLTRANSFERASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

POLYSIALIC ACID O-ACETYLTRANSFERASE

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