SMTL ID : 2dti.1

Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-AMP, Pyrophosphate and Mn(2+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: N.103, D.104, K.111 Ligands: POP.2, BT5.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.104, A:D.104 MN.3: 5 residues within 4Å: Chain B: N.103, D.104, K.111 Ligands: BT5.5, POP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.104, B:D.104

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.2: 12 residues within 4Å: Chain A: R.48, R.51, K.100, P.102, N.103, D.104, K.111, V.230, S.231, L.232 Ligands: MN.1, BT5.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:V.230, A:L.232 Salt bridges: A:R.48, A:R.51, A:R.51, A:K.100, A:K.100, A:K.111, A:K.111 POP.6: 8 residues within 4Å: Chain B: R.48, K.100, D.104, K.111, S.231, L.232 Ligands: MN.3, BT5.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:L.232 Water bridges: B:R.48, B:R.48, B:K.111, B:K.111 Salt bridges: B:R.48, B:K.100, B:K.100, B:K.111

2 x BT5: BIOTINYL-5-AMP(Non-covalent)

BT5.4: 28 residues within 4Å: Chain A: S.21, T.22, N.23, Q.42, G.45, H.46, G.47, R.48, R.51, K.52, W.53, E.54, W.61, L.62, S.63, N.103, D.104, K.111, G.114, V.115, I.128, G.129, N.131, V.136, P.137, A.140 Ligands: MN.1, POP.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:W.53, A:W.53 Hydrogen bonds: A:T.22, A:T.22, A:N.23, A:Q.42, A:H.46, A:H.46, A:R.48, A:E.54, A:N.103, A:V.115, A:N.131, A:N.131 Water bridges: A:K.52 Salt bridges: A:R.51, A:K.111, A:K.111 pi-Stacking: A:W.53, A:W.53 BT5.5: 28 residues within 4Å: Chain B: S.21, T.22, N.23, Q.42, G.45, H.46, G.47, R.48, R.51, K.52, W.53, E.54, W.61, L.62, S.63, N.103, D.104, K.111, G.114, V.115, L.116, I.128, G.129, N.131, P.137, A.140 Ligands: MN.3, POP.6 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:W.53, B:W.53, B:L.116 Hydrogen bonds: B:T.22, B:T.22, B:N.23, B:Q.42, B:H.46, B:H.46, B:R.48, B:E.54, B:N.103, B:K.111, B:N.131, B:N.131 Water bridges: B:R.48, B:R.48 Salt bridges: B:K.111, B:K.111 pi-Stacking: B:W.53, B:W.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bagautdinov, B. et al., Ligand Structures Of Biotin Protein Ligase From Pyrococcus Horikoshii OT3. To be Published

Release Date

2007-01-12

Peptides

235aa long hypothetical biotin-[acetyl-CoA-carboxylase] ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

235aa long hypothetical biotin-[acetyl-CoA-carboxylase] ligase

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