SMTL ID : 1ynr.1

Crystal structure of the cytochrome c-552 from Hydrogenobacter thermophilus at 2.0 resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: Q.7, K.8, E.68 Chain B: K.6 Chain C: K.20 8 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C, 3 interactions with chain A Water bridges: B:K.6, C:K.20, C:K.20, A:Q.7, A:N.63 Salt bridges: B:K.6, C:K.20, A:K.8 SO4.6: 3 residues within 4Å: Chain B: K.47, T.65, D.66 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.66 Water bridges: B:T.65, B:A.67 Salt bridges: B:K.47 SO4.10: 5 residues within 4Å: Chain A: K.20 Chain C: Q.7, K.8, E.68 Chain D: K.6 7 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C, 3 interactions with chain A Salt bridges: D:K.6, C:K.8, A:K.20 Water bridges: C:N.63, C:N.63, A:K.20, A:K.20

4 x HEC: HEME C(Covalent)

HEC.2: 26 residues within 4Å: Chain A: G.9, C.10, C.13, H.14, V.21, G.22, P.23, V.28, Y.32, Y.41, L.42, K.45, I.46, G.50, S.51, G.52, V.53, W.54, G.55, V.57, M.59, P.60, Q.62, I.76 Chain D: N.63 Ligands: MPD.4 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:V.21, A:P.23, A:V.28, A:V.28, A:L.42, A:K.45, A:V.57, A:M.59, A:P.60, A:Q.62, A:I.76 Hydrogen bonds: A:Y.32, A:Y.41, A:G.52, A:V.53, A:W.54, A:G.55 Water bridges: A:G.55, A:V.57 Salt bridges: A:K.31 Metal complexes: A:H.14 HEC.7: 27 residues within 4Å: Chain B: C.10, C.13, H.14, V.21, G.22, P.23, Y.25, V.28, Y.32, Y.41, L.42, K.45, I.46, G.50, S.51, G.52, V.53, W.54, G.55, V.57, P.58, M.59, P.60, Q.62, V.64, L.72, I.76 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:Y.25, B:V.28, B:L.42, B:I.46, B:V.57, B:M.59, B:P.60, B:Q.62, B:V.64, B:L.72, B:I.76 Hydrogen bonds: B:Y.32, B:Y.41, B:G.52, B:V.53, B:W.54, B:G.55 Water bridges: B:G.55 Metal complexes: B:H.14 HEC.11: 27 residues within 4Å: Chain B: N.63 Chain C: G.9, C.10, C.13, H.14, V.21, G.22, P.23, V.28, Y.32, Y.41, L.42, K.45, I.46, G.50, S.51, G.52, V.53, W.54, G.55, V.57, M.59, P.60, Q.62, L.72, I.76 Ligands: MPD.8 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:P.23, C:V.28, C:L.42, C:K.45, C:I.46, C:M.59, C:P.60, C:Q.62, C:L.72 Hydrogen bonds: C:Y.32, C:Y.41, C:G.52, C:V.53, C:W.54, C:G.55, C:V.57 Salt bridges: C:K.45 Metal complexes: C:H.14 HEC.14: 26 residues within 4Å: Chain D: C.10, C.13, H.14, V.21, G.22, P.23, V.28, Y.32, Y.41, L.42, K.45, I.46, G.50, S.51, G.52, V.53, W.54, G.55, V.57, P.58, M.59, P.60, Q.62, V.64, L.72, I.76 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:V.28, D:L.42, D:K.45, D:I.46, D:W.54, D:V.57, D:M.59, D:P.60, D:Q.62, D:V.64, D:I.76 Hydrogen bonds: D:Y.32, D:Y.41, D:G.52, D:V.53, D:W.54, D:G.55 Water bridges: D:G.55, D:V.57 Metal complexes: D:H.14

8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 9 residues within 4Å: Chain A: K.19, K.20, V.21, G.22, P.23, W.54 Chain D: K.8, N.63, V.64 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:K.19, A:W.54 Water bridges: A:K.19, D:K.8 MPD.4: 7 residues within 4Å: Chain A: A.12, C.13, V.21 Chain C: N.63 Chain D: G.9, A.12 Ligands: HEC.2 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: D:A.12, A:A.12, A:V.21, C:N.63 Water bridges: C:Q.62 MPD.5: 5 residues within 4Å: Chain A: Y.32, R.35, D.37, A.38, Y.41 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.32, A:Y.41 Hydrogen bonds: A:D.37 MPD.8: 7 residues within 4Å: Chain A: P.61 Chain B: G.9, A.12 Chain C: A.12, C.13, V.21 Ligands: HEC.11 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:Q.62 Hydrophobic interactions: C:V.21 MPD.9: 6 residues within 4Å: Chain B: Y.32, R.35, K.36, D.37, A.38, Y.41 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.41, B:Y.41 Hydrogen bonds: B:R.35, B:R.35 MPD.12: 8 residues within 4Å: Chain B: K.8, N.63, V.64 Chain C: K.19, K.20, V.21, P.23, W.54 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.54 MPD.13: 3 residues within 4Å: Chain C: Y.32, R.35, Y.41 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.32, C:R.35, C:Y.41, C:Y.41, C:Y.41 MPD.15: 5 residues within 4Å: Chain D: Y.32, R.35, K.36, A.38, Y.41 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.32, D:Y.32, D:Y.41 Hydrogen bonds: D:R.35, D:K.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Travaglini-Allocatelli, C. et al., An Obligatory Intermediate in the Folding Pathway of Cytochrome c552 from Hydrogenobacter thermophilus. J.Biol.Chem. (2005)

Release Date

2005-05-17

Peptides

Cytochrome c-552: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cytochrome c-552

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