SMTL ID : 4hbf.2 (1 other biounit)

Crystal structure of PpcA V13A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

6 x HEC: HEME C(Non-covalent)(Covalent)

HEC.1: 17 residues within 4Å: Chain A: A.1, D.2, D.3, I.4, F.15, H.17, H.20, Q.21, V.24, C.27, C.30, H.31 Chain B: I.38, E.39 Ligands: HEC.2, DXC.4, DXC.11 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:I.4, A:F.15, A:F.15, A:V.24, B:I.38 Hydrogen bonds: A:D.3, A:I.4, A:F.15 Water bridges: A:A.1, A:A.1, A:A.1 Salt bridges: A:H.17 Metal complexes: A:H.17, A:H.31 HEC.2: 21 residues within 4Å: Chain A: L.6, K.14, F.15, P.16, A.19, H.20, A.23, V.24, K.29, F.41, K.49, G.50, C.51, C.54, H.55, M.58, K.60, G.61, P.62 Ligands: HEC.1, DXC.4 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:L.6, A:A.19, A:K.29, A:F.41, A:K.60, A:P.62 Water bridges: A:G.61 Salt bridges: A:K.60 pi-Stacking: A:F.15 Metal complexes: A:H.20, A:H.55 HEC.3: 21 residues within 4Å: Chain A: L.6, A.8, K.9, N.10, A.13, F.41, G.42, K.43, A.46, H.47, C.51, K.52, H.55, P.62, T.63, K.64, C.65, C.68, H.69 Chain B: A.1, D.2 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:L.6, A:A.8, A:A.13, A:F.41, A:K.43, A:A.46, A:K.52 Hydrogen bonds: A:K.7, A:K.9, B:D.2 Water bridges: A:K.43, B:D.2 Salt bridges: A:K.9 pi-Cation interactions: A:K.43 Metal complexes: A:H.47, A:H.69 HEC.8: 17 residues within 4Å: Chain A: I.38, E.39 Chain B: A.1, D.2, D.3, I.4, F.15, H.17, H.20, Q.21, V.24, C.27, C.30, H.31 Ligands: DXC.4, HEC.9, DXC.11 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:I.4, B:F.15, B:F.15, B:V.24, A:I.38 Hydrogen bonds: B:A.1, B:I.4, B:F.15 Water bridges: B:A.1 Salt bridges: B:H.17 Metal complexes: B:H.17, B:H.31 HEC.9: 21 residues within 4Å: Chain B: L.6, K.14, F.15, P.16, A.19, H.20, A.23, V.24, K.29, F.41, K.49, G.50, C.51, C.54, H.55, M.58, K.60, G.61, P.62 Ligands: HEC.8, DXC.11 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:L.6, B:A.19, B:K.29, B:F.41, B:K.60, B:P.62 Water bridges: B:G.61 Salt bridges: B:K.60 pi-Stacking: B:F.15 Metal complexes: B:H.20, B:H.55 HEC.10: 21 residues within 4Å: Chain A: A.1, D.2 Chain B: L.6, A.8, K.9, N.10, A.13, F.41, G.42, K.43, A.46, H.47, C.51, K.52, H.55, P.62, T.63, K.64, C.65, C.68, H.69 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:L.6, B:A.8, B:A.13, B:F.41, B:K.43, B:A.46, B:K.52 Hydrogen bonds: B:K.7, B:K.9, A:D.2, A:D.2 Water bridges: B:K.43, A:D.2 Salt bridges: B:K.9 pi-Cation interactions: B:K.43 Metal complexes: B:H.47, B:H.69

2 x DXC: (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID(Non-covalent)

DXC.4: 14 residues within 4Å: Chain A: I.4, L.6, K.29, C.30, K.37, I.38, F.41, M.45, K.49, G.50 Ligands: HEC.1, HEC.2, HEC.8, DXC.11 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.4, A:K.37, A:F.41, A:F.41, A:F.41 Water bridges: A:F.41 Salt bridges: A:K.33, A:K.37, A:K.49 DXC.11: 14 residues within 4Å: Chain B: I.4, L.6, K.29, C.30, K.37, I.38, F.41, M.45, K.49, G.50 Ligands: HEC.1, DXC.4, HEC.8, HEC.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.4, B:K.37, B:F.41, B:F.41, B:F.41 Water bridges: B:F.41 Salt bridges: B:K.33, B:K.37, B:K.49

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

SO4.5: 7 residues within 4Å: Chain A: P.35, G.36, K.37, I.38, E.39 Chain B: H.31, E.32 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.32, A:G.36, A:I.38, A:E.39 Water bridges: B:K.33 Salt bridges: B:H.31 SO4.6: 2 residues within 4Å: Chain A: K.28, E.32 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.28 SO4.7: 3 residues within 4Å: Chain A: G.42, K.43, E.44 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:A.1, A:K.43, A:E.44 Water bridges: A:M.45 SO4.12: 7 residues within 4Å: Chain A: H.31, E.32 Chain B: P.35, G.36, K.37, I.38, E.39 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.36, B:I.38, B:E.39, B:E.39, A:E.32 Water bridges: A:K.33 Salt bridges: A:H.31 SO4.13: 2 residues within 4Å: Chain B: K.28, E.32 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.28 SO4.14: 3 residues within 4Å: Chain B: G.42, K.43, E.44 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.43, B:E.44, A:A.1 Water bridges: B:M.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pokkuluri, P.R. et al., V13 mutants of PpcA. To be Published

Release Date

2012-10-31

Peptides

PpcA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PpcA

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