SMTL ID : 3ojo.1

Derivative structure of the UDP-N-acetyl-mannosamine dehydrogenase Cap5O from S. aureus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 21 residues within 4Å: Chain A: V.17, G.18, L.19, G.20, Y.21, I.22, V.40, D.41, I.42, N.43, A.90, V.91, P.92, T.93, L.107, S.129, T.130, E.162, V.164, H.268, R.333 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:L.19, A:Y.21, A:I.22, A:I.42, A:T.93, A:T.93, A:L.107, A:T.130, A:V.164 Water bridges: A:G.20, A:G.20 Salt bridges: A:R.333, A:R.333 NAD.8: 22 residues within 4Å: Chain B: V.17, G.18, L.19, G.20, Y.21, I.22, V.40, D.41, I.42, N.43, A.90, V.91, P.92, T.93, L.107, A.111, S.129, T.130, E.162, R.163, V.164, R.333 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.22 Hydrogen bonds: B:L.19, B:Y.21, B:I.22, B:I.42, B:T.93, B:T.93, B:L.107, B:T.130, B:T.130, B:V.164 Water bridges: B:G.20, B:G.23, B:N.43, B:T.46 Salt bridges: B:R.333

6 x PDC: PYRIDINE-2,6-DICARBOXYLIC ACID(Non-covalent)

PDC.2: 8 residues within 4Å: Chain A: L.165, R.222, Y.325, K.326 Chain B: R.255 Ligands: PDC.3, PDC.4, EU.5 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.325, A:K.326, A:K.326 Salt bridges: A:R.222, B:R.255 pi-Cation interactions: A:K.326 Hydrogen bonds: B:R.255 Water bridges: B:R.255, B:R.255 PDC.3: 9 residues within 4Å: Chain A: R.163, V.164, L.165, E.172, K.326 Chain B: H.253 Ligands: PDC.2, PDC.4, EU.5 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:R.163 Salt bridges: A:R.163, A:K.326, B:H.253, B:R.255 Water bridges: B:R.255 PDC.4: 10 residues within 4Å: Chain A: R.163, E.218, N.219, R.222 Chain B: H.253, R.255, V.256 Ligands: PDC.2, PDC.3, EU.5 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:E.218, A:R.222, B:V.256 Hydrogen bonds: A:N.219, B:R.255 Salt bridges: A:R.163, A:R.222, B:H.253, B:R.255 pi-Cation interactions: A:R.222, B:H.253 PDC.7: 6 residues within 4Å: Chain A: R.255 Chain B: R.222, K.326 Ligands: EU.6, PDC.9, PDC.10 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.255, B:R.222, B:H.268, B:K.326 PDC.9: 9 residues within 4Å: Chain A: H.253, R.255 Chain B: R.163, V.164, E.172, K.326 Ligands: EU.6, PDC.7, PDC.10 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Salt bridges: A:H.253, A:R.255, B:R.163, B:K.326 Hydrophobic interactions: B:R.163 PDC.10: 10 residues within 4Å: Chain A: H.253, R.255, V.256 Chain B: R.163, E.218, N.219, R.222 Ligands: EU.6, PDC.7, PDC.9 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.256, B:E.218, B:R.222 Salt bridges: A:H.253, A:H.253, A:R.255, B:R.163, B:R.222 pi-Cation interactions: A:H.253

2 x EU: EUROPIUM ION(Non-functional Binders)

EU.5: 3 residues within 4Å: Ligands: PDC.2, PDC.3, PDC.4 No protein-ligand interaction detected (PLIP) EU.6: 3 residues within 4Å: Ligands: PDC.7, PDC.9, PDC.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gruszczyk, J. et al., Structure Analysis of the Staphylococcus aureus UDP-N-acetyl-mannosamine Dehydrogenase Cap5O Involved in Capsular Polysaccharide Biosynthesis. J.Biol.Chem. (2011)

Release Date

2011-03-23

Peptides

Cap5O: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cap5O

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