SMTL ID : 9cuf.1

Room temperature SSX structure of ccNiR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-dimer

Ligands

10 x HEC: HEME C(Covalent)

HEC.1: 21 residues within 4Å: Chain A: D.53, Y.54, K.55, A.56, P.57, D.66, V.67, T.70, R.72, T.73, L.84, A.87, C.88, C.91, K.92, C.171, H.172, Y.175, H.226, H.350 Ligands: HEC.3 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:K.55, A:P.57, A:D.66, A:V.67, A:T.70, A:T.73, A:L.84, A:Y.175, A:Y.175, A:H.226 Hydrogen bonds: A:K.55 Salt bridges: A:R.72, A:H.226, A:H.350 pi-Stacking: A:H.226 pi-Cation interactions: A:K.92 HEC.2: 18 residues within 4Å: Chain A: N.8, F.15, Q.18, Y.19, W.22, G.125, C.126, C.129, H.130, P.135, L.137, K.160, V.245, M.249, F.260, T.261, H.263 Ligands: HEC.3 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:F.15, A:F.15, A:Q.18, A:Q.18, A:Y.19, A:W.22, A:P.135, A:L.137, A:V.245 Hydrogen bonds: A:Q.18, A:T.261, A:T.261 Salt bridges: A:K.160 pi-Stacking: A:H.130 Metal complexes: A:H.130, A:H.263 HEC.3: 24 residues within 4Å: Chain A: S.28, P.57, R.58, G.59, H.60, Y.62, A.63, D.66, C.91, K.92, I.124, V.167, C.168, Q.170, C.171, H.172, C.244, H.248, M.249, V.265, G.266 Ligands: HEC.1, HEC.2, HEC.4 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:K.92, A:I.124, A:I.124 Hydrogen bonds: A:S.28, A:R.58, A:G.59, A:V.265 Metal complexes: A:H.60 HEC.4: 17 residues within 4Å: Chain A: P.57, H.172, E.228, W.232, H.237, V.242, S.243, C.244, C.247, H.248, P.268, K.295, H.350, A.354, H.355 Ligands: HEC.3, HEC.5 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:H.172, A:E.228, A:E.228, A:W.232, A:P.268, A:A.354 Salt bridges: A:K.295 Metal complexes: A:H.248 HEC.5: 19 residues within 4Å: Chain A: I.236, H.237, N.240, V.242, D.246, P.268, F.269, T.275, C.276, T.278, C.279, H.280, L.287, R.294, H.355 Chain B: H.280, Q.282 Ligands: HEC.4, HEC.11 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain A, Hydrogen bonds: B:Q.282, B:Q.282 Salt bridges: B:H.280, A:H.237, A:R.294 Hydrophobic interactions: A:N.240, A:P.268, A:F.269, A:L.287 pi-Cation interactions: A:H.237 Metal complexes: A:H.237 HEC.7: 18 residues within 4Å: Chain B: D.53, K.55, P.57, T.70, R.72, L.84, A.87, C.88, S.90, C.91, K.92, C.171, H.172, Y.175, H.226, A.348, H.350 Ligands: HEC.9 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:K.55, B:P.57, B:P.57, B:T.70, B:L.84, B:Y.175, B:Y.175, B:H.226 Hydrogen bonds: B:D.53, B:K.55, B:A.348 Salt bridges: B:R.72, B:H.226, B:H.350 pi-Stacking: B:H.226 pi-Cation interactions: B:K.92 HEC.8: 19 residues within 4Å: Chain B: Y.11, F.15, Q.18, Y.19, W.22, G.125, C.126, C.129, H.130, P.135, L.137, E.164, V.167, M.249, K.251, F.260, T.261, H.263 Ligands: HEC.9 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:Y.11, B:F.15, B:F.15, B:F.15, B:Y.19, B:P.135, B:L.137, B:V.167 Hydrogen bonds: B:Q.18, B:T.261, B:T.261 Salt bridges: B:K.251, B:K.251 pi-Stacking: B:H.130, B:H.263 pi-Cation interactions: B:H.130 Metal complexes: B:H.263 HEC.9: 23 residues within 4Å: Chain B: S.28, P.57, R.58, G.59, H.60, Y.62, D.66, C.91, K.92, I.124, D.128, V.167, C.168, Q.170, C.171, H.172, H.248, M.249, V.265, G.266 Ligands: HEC.7, HEC.8, HEC.10 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:P.57, B:K.92, B:I.124, B:H.248, B:V.265, B:V.265 Hydrogen bonds: B:S.28, B:R.58, B:G.59, B:D.66, B:V.265 Metal complexes: B:H.172 HEC.10: 20 residues within 4Å: Chain B: P.57, C.168, H.172, W.232, H.237, V.242, S.243, C.244, C.247, H.248, N.267, P.268, F.269, K.295, H.350, G.351, A.354, H.355 Ligands: HEC.9, HEC.11 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:H.172, B:F.269, B:A.354 Hydrogen bonds: B:N.267 Salt bridges: B:K.295 pi-Stacking: B:H.355 Metal complexes: B:H.248 HEC.11: 15 residues within 4Å: Chain A: H.280, Q.282 Chain B: I.236, H.237, N.240, V.242, F.269, T.275, C.276, C.279, H.280, L.287, R.294 Ligands: HEC.5, HEC.10 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B, Hydrogen bonds: A:Q.282, B:I.236, B:H.237 Salt bridges: A:H.280, B:H.237, B:R.294 Hydrophobic interactions: B:V.242, B:F.269 pi-Stacking: B:H.280 Metal complexes: B:H.280

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: E.174, Y.175, Y.176, Y.204, D.211, K.223 No protein-ligand interaction detected (PLIP) CA.12: 6 residues within 4Å: Chain B: E.174, Y.175, Y.176, Y.204, D.211, K.223 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Y.175, B:K.223

1 x PE3: 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL(Non-functional Binders)

PE3.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malla, T.N. et al., Exploiting fourth-generation synchrotron radiation for enzyme and photoreceptor characterization. Iucrj (2025)

Release Date

2025-01-15

Peptides

Cytochrome c-552: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytochrome c-552

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