SMTL ID : 3zpg.1

Acinetobacter baumannii RibD, form 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.75, C.100, C.109 Ligands: CAC.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.75, A:C.100, A:C.109 ZN.11: 4 residues within 4Å: Chain B: H.75, C.100, C.109 Ligands: CAC.17 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.75, B:C.100, B:C.109

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.209, C.227, Q.228, L.229, R.232 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.228, A:L.229 Salt bridges: A:R.209, A:R.232 SO4.3: 4 residues within 4Å: Chain A: H.75, G.104, R.105, T.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.104, A:R.105, A:T.106 Salt bridges: A:H.75 SO4.12: 5 residues within 4Å: Chain B: R.209, C.227, Q.228, L.229, R.232 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.228, B:L.229 Salt bridges: B:R.209, B:R.232 SO4.13: 4 residues within 4Å: Chain B: H.75, G.104, R.105, T.106 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.104, B:R.105, B:T.106 Salt bridges: B:H.75

4 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.4: 10 residues within 4Å: Chain A: L.250, R.252, M.272, P.291, L.292, T.315, L.316, A.319, E.323 Ligands: OXL.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.252, A:R.252, A:L.292 Water bridges: A:E.323, A:E.323 pi-Cation interactions: A:R.252, A:R.252 5GP.10: 7 residues within 4Å: Chain A: K.158, D.204, H.207, W.208, D.363, R.372, R.374 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.372, A:R.372 Water bridges: A:Y.44, A:Y.44, A:H.207 Salt bridges: A:K.158, A:R.374 pi-Stacking: A:H.207, A:H.207 pi-Cation interactions: A:H.207 5GP.14: 10 residues within 4Å: Chain B: L.250, R.252, M.272, P.291, L.292, T.315, L.316, A.319, E.323 Ligands: OXL.16 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.252, B:R.252, B:L.292 Water bridges: B:E.323, B:E.323 pi-Cation interactions: B:R.252, B:R.252 5GP.20: 7 residues within 4Å: Chain B: K.158, D.204, H.207, W.208, D.363, R.372, R.374 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.372, B:R.372 Water bridges: B:Y.44, B:H.207, B:H.207 Salt bridges: B:K.158, B:R.374 pi-Stacking: B:H.207, B:H.207 pi-Cation interactions: B:H.207

4 x OXL: OXALATE ION(Non-covalent)

OXL.5: 4 residues within 4Å: Chain A: G.66, F.67, P.69, F.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.67 OXL.6: 7 residues within 4Å: Chain A: I.219, L.250, D.251, R.252, R.253, R.255 Ligands: 5GP.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.252, A:R.253 Water bridges: A:I.219, A:G.254, A:R.255 Salt bridges: A:R.252, A:R.253, A:R.255 OXL.15: 4 residues within 4Å: Chain B: G.66, F.67, P.69, F.79 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.67 OXL.16: 7 residues within 4Å: Chain B: I.219, L.250, D.251, R.252, R.253, R.255 Ligands: 5GP.14 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.252, B:R.253 Water bridges: B:I.219, B:G.254, B:R.255 Salt bridges: B:R.252, B:R.253, B:R.255

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.7: 9 residues within 4Å: Chain A: V.52, H.75, E.77, L.97, E.98, P.99, C.100, C.109 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.76, A:C.100 CAC.17: 9 residues within 4Å: Chain B: V.52, H.75, E.77, L.97, E.98, P.99, C.100, C.109 Ligands: ZN.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.75, B:A.76, B:C.100

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

CL.8: 4 residues within 4Å: Chain A: G.218, T.221, A.312, G.313 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: G.218, T.221, A.312, G.313 Ligand excluded by PLIP

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

ACT.9: 8 residues within 4Å: Chain A: L.43, K.158, L.159, N.160, Q.161, G.162, R.175, D.307 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.43 Hydrogen bonds: A:K.158, A:Q.161, A:Q.161, A:G.162 Salt bridges: A:R.175 ACT.19: 8 residues within 4Å: Chain B: L.43, K.158, L.159, N.160, Q.161, G.162, R.175, D.307 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.43 Hydrogen bonds: B:K.158, B:Q.161, B:Q.161, B:G.162 Salt bridges: B:R.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dawson, A. et al., Structure of Diaminohydroxyphosphoribosylaminopyrimidine Deaminase/5-Amino-6-(5-Phosphoribosylamino)Uracil Reductase from Acinetobacter Baumannii. Acta Crystallogr.,Sect.F (2013)

Release Date

2013-03-27

Peptides

RIBD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

RIBD

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