SMTL ID : 7c90.1

Crystal structure of Cytochrome CL from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT (Ma-CytcL)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-tetramer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 24 residues within 4Å: Chain A: A.87, C.88, C.91, H.92, L.100, G.101, P.102, L.104, Y.109, T.110, Y.111, N.114, L.120, T.123, I.124, A.128, R.129, M.131, M.132, Q.135, L.139, I.147 Chain B: L.100 Chain D: G.90 23 PLIP interactions: 22 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:A.87, A:L.100, A:P.102, A:L.104, A:L.104, A:L.120, A:T.123, A:I.124, A:M.131, A:M.132, A:Q.135, A:L.139, A:I.147, B:L.100 Hydrogen bonds: A:T.110, A:T.110, A:Y.111, A:Y.111, A:N.114, A:R.129 Water bridges: A:A.103, A:T.110 Metal complexes: A:H.92 HEC.9: 24 residues within 4Å: Chain B: A.87, C.88, C.91, H.92, G.101, P.102, L.104, Y.109, T.110, Y.111, N.114, L.120, T.123, I.124, A.128, R.129, S.130, M.131, M.132, Q.135, L.139, I.147 Chain C: G.90, C.91 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:P.102, B:L.104, B:L.104, B:L.120, B:T.123, B:I.124, B:M.132, B:L.139, B:I.147 Hydrogen bonds: B:T.110, B:Y.111, B:N.114, B:R.129 Metal complexes: B:H.92 HEC.17: 24 residues within 4Å: Chain B: G.90, C.91 Chain C: A.87, C.88, C.91, H.92, L.100, G.101, P.102, L.104, Y.109, T.110, Y.111, N.114, L.120, T.123, I.124, A.128, R.129, M.131, M.132, Q.135, I.147 Chain D: L.100 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: C:A.87, C:L.100, C:P.102, C:L.104, C:L.104, C:L.120, C:T.123, C:I.124, C:I.124, C:M.131, C:M.132, C:Q.135, C:I.147, D:L.100 Hydrogen bonds: C:T.110, C:Y.111, C:N.114, C:R.129, C:R.129 Water bridges: C:T.110, C:R.129 Metal complexes: C:H.92 HEC.23: 23 residues within 4Å: Chain A: G.90, C.91 Chain D: A.87, C.88, C.91, H.92, G.101, P.102, L.104, Y.109, T.110, Y.111, N.114, L.120, T.123, I.124, A.128, R.129, S.130, M.131, M.132, L.139, I.147 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:A.87, D:L.104, D:L.104, D:L.120, D:T.123, D:I.124, D:M.131, D:M.132, D:L.139, D:I.147 Hydrogen bonds: D:T.110, D:T.110, D:Y.111, D:Y.111, D:N.114, D:R.129 Metal complexes: D:H.92

4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 4 residues within 4Å: Chain A: D.46, F.49, Y.125, Y.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.125 EPE.10: 2 residues within 4Å: Chain B: D.73, E.75 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.73 Salt bridges: B:E.75 EPE.11: 5 residues within 4Å: Chain B: V.44, L.45, D.46, L.47, S.48 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.46, B:L.47, B:S.48 Salt bridges: B:D.46, B:D.46 EPE.18: 7 residues within 4Å: Chain C: E.54, K.55, T.56, V.59, T.140, K.141, D.142 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.56, C:T.56, C:T.140, C:K.141, C:D.142 Water bridges: C:K.141 Salt bridges: C:E.54

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain B: F.182 No protein-ligand interaction detected (PLIP) GOL.4: 2 residues within 4Å: Chain A: Y.108 Chain B: T.39 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.39, A:Y.108, A:Y.108 GOL.12: 5 residues within 4Å: Chain B: V.44, L.45, D.46, Y.125, Y.136 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.44, B:D.46, B:Y.136

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 2 residues within 4Å: Chain A: P.112, K.113 No protein-ligand interaction detected (PLIP) CA.13: 2 residues within 4Å: Chain B: P.112, K.113 No protein-ligand interaction detected (PLIP) CA.19: 2 residues within 4Å: Chain C: P.112, K.113 No protein-ligand interaction detected (PLIP) CA.24: 2 residues within 4Å: Chain D: P.112, K.113 No protein-ligand interaction detected (PLIP)

4 x FE: FE (III) ION(Non-covalent)

FE.6: 2 residues within 4Å: Chain A: H.94, E.97 No protein-ligand interaction detected (PLIP) FE.14: 2 residues within 4Å: Chain B: H.94, K.99 No protein-ligand interaction detected (PLIP) FE.20: 2 residues within 4Å: Chain C: H.94, E.97 No protein-ligand interaction detected (PLIP) FE.25: 2 residues within 4Å: Chain D: H.94, E.97 No protein-ligand interaction detected (PLIP)

8 x NA: SODIUM ION(Non-functional Binders)

NA.7: 4 residues within 4Å: Chain A: D.106, Y.108, Y.109 Ligands: NA.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.106, A:D.106 Water bridges: A:Y.109 NA.8: 4 residues within 4Å: Chain A: A.103, D.106, Y.108 Ligands: NA.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.106 NA.15: 4 residues within 4Å: Chain B: A.103, D.106, Y.108 Ligands: NA.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.106 Water bridges: B:T.110 NA.16: 5 residues within 4Å: Chain B: L.104, D.106, Y.108, Y.109 Ligands: NA.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.106, B:D.106 NA.21: 4 residues within 4Å: Chain C: D.106, Y.108, Y.109 Ligands: NA.22 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.106, C:Y.109 NA.22: 4 residues within 4Å: Chain C: A.103, D.106, Y.108 Ligands: NA.21 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.108 Water bridges: C:A.103 NA.26: 4 residues within 4Å: Chain D: A.103, D.106, Y.108 Ligands: NA.27 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.103 Water bridges: D:T.110 NA.27: 5 residues within 4Å: Chain D: L.104, D.106, Y.108, Y.109 Ligands: NA.26 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.106, D:D.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, S. et al., Crystal Structure of CytochromecLfrom the Aquatic Methylotrophic BacteriumMethylophaga aminisulfidivoransMPT. J Microbiol Biotechnol. (2020)

Release Date

2020-07-22

Peptides

Cytochrome c, mono-and diheme variant: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cytochrome c, mono-and diheme variant