SMTL ID : 2ylg.1

CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: ASCORBATE AND CARBON MONOOXIDE BOUND L16A VARIANT AT 1.05 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 32 residues within 4Å: Chain A: V.9, R.12, Q.13, A.16, T.17, M.19, A.20, F.23, L.48, S.52, W.56, F.59, G.65, G.66, D.67, A.68, I.72, F.79, K.82, Q.83, F.86, I.90, V.112, S.115, C.116, C.119, H.120, Y.123, R.124 Ligands: CMO.2, ASC.3, SO4.4 27 PLIP interactions: 23 interactions with chain A, 3 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:A.16, A:W.56, A:W.56, A:F.59, A:I.72, A:F.79, A:K.82, A:Q.83, A:F.86, A:F.86, A:R.124 Hydrogen bonds: A:Q.13, A:T.17, A:D.67, A:A.68 Water bridges: A:T.17, A:D.67, A:D.67, B:K.10, B:K.10, B:K.10 Salt bridges: A:R.12 pi-Stacking: A:H.120, A:H.120 pi-Cation interactions: A:R.124 Metal complexes: A:H.120, CMO.2 HEC.6: 32 residues within 4Å: Chain B: V.9, R.12, Q.13, A.16, T.17, M.19, A.20, F.23, L.48, S.52, W.56, F.59, G.65, G.66, D.67, A.68, I.72, F.79, K.82, Q.83, F.86, I.90, V.112, S.115, C.116, C.119, H.120, Y.123, R.124 Ligands: CMO.7, ASC.8, SO4.9 26 PLIP interactions: 22 interactions with chain B, 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:A.16, B:W.56, B:W.56, B:F.59, B:I.72, B:F.79, B:K.82, B:Q.83, B:F.86, B:F.86, B:R.124 Hydrogen bonds: B:Q.13, B:T.17, B:D.67, B:A.68 Water bridges: B:T.17, B:D.67, A:K.10, A:K.10, A:K.10 Salt bridges: B:R.12 pi-Stacking: B:H.120, B:H.120 pi-Cation interactions: B:R.124 Metal complexes: B:H.120, CMO.7

2 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.2: 6 residues within 4Å: Chain A: A.16, M.19, P.55, W.56, H.120 Ligands: HEC.1 No protein-ligand interaction detected (PLIP) CMO.7: 6 residues within 4Å: Chain B: A.16, M.19, P.55, W.56, H.120 Ligands: HEC.6 No protein-ligand interaction detected (PLIP)

2 x ASC: ASCORBIC ACID(Non-covalent)

ASC.3: 10 residues within 4Å: Chain A: A.20, F.23, G.24, G.113, C.116, K.117, H.120, R.124 Ligands: HEC.1, SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.120 Water bridges: A:G.113, A:R.124 ASC.8: 10 residues within 4Å: Chain B: A.20, F.23, G.24, G.113, C.116, K.117, H.120, R.124 Ligands: HEC.6, SO4.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.120 Water bridges: B:G.113, B:R.124

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

SO4.4: 4 residues within 4Å: Chain A: H.120, R.124 Ligands: HEC.1, ASC.3 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.124 Salt bridges: A:H.120, A:R.124 SO4.5: 3 residues within 4Å: Chain A: R.69, K.125, K.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.126 Water bridges: A:R.69, A:R.69 Salt bridges: A:R.69 SO4.9: 4 residues within 4Å: Chain B: H.120, R.124 Ligands: HEC.6, ASC.8 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.124 Salt bridges: B:H.120, B:R.124 SO4.10: 3 residues within 4Å: Chain B: R.69, K.125, K.126 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.126 Water bridges: B:R.69, B:R.69 Salt bridges: B:R.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antonyuk, S.V. et al., Carbon Monoxide Poisoning is Prevented by the Energy Costs of Conformational Changes in Gas- Binding Haemproteins. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-10-05

Peptides

CYTOCHROME C': AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CYTOCHROME C'

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