SMTL ID : 6iyi.1

X-ray sequence and high resolution crystal structure of Starry sturgeon methemoglobin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-mer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 17 residues within 4Å: Chain A: M.32, Y.42, F.43, H.45, Y.46, H.59, K.62, A.66, L.67, L.84, H.88, L.92, V.94, N.98, F.99, L.102, L.137 21 PLIP interactions: 20 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:Y.42, A:F.43, A:F.43, A:K.62, A:A.66, A:L.84, A:L.92, A:L.92, A:V.94, A:V.94, A:L.102, A:L.137 Hydrogen bonds: A:Y.46 Water bridges: A:H.59, A:H.59 Salt bridges: A:H.45, A:H.59, A:K.62 pi-Stacking: A:H.59 Metal complexes: A:H.88, H2O.2 HEM.2: 16 residues within 4Å: Chain B: T.38, Y.41, F.42, A.44, F.45, H.63, V.67, S.70, L.88, H.92, L.96, V.98, N.102, F.103, F.106, L.141 16 PLIP interactions: 15 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:T.38, B:Y.41, B:F.42, B:F.42, B:V.67, B:L.88, B:L.88, B:L.96, B:V.98, B:F.103, B:F.106, B:L.141 Water bridges: B:H.63 pi-Stacking: B:H.63 Metal complexes: B:H.92, H2O.7 HEM.4: 17 residues within 4Å: Chain C: M.32, Y.42, F.43, H.45, Y.46, H.59, K.62, A.66, L.67, L.84, H.88, L.92, V.94, N.98, F.99, L.102, L.137 18 PLIP interactions: 17 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:Y.42, C:F.43, C:F.43, C:K.62, C:A.66, C:L.84, C:L.92, C:L.92, C:V.94, C:V.94, C:L.102, C:L.137 Salt bridges: C:H.45, C:H.59, C:K.62 pi-Stacking: C:H.59 Metal complexes: C:H.88, H2O.14 HEM.5: 16 residues within 4Å: Chain D: T.38, Y.41, F.42, A.44, F.45, H.63, V.67, S.70, L.88, H.92, L.96, V.98, N.102, F.103, F.106, L.141 15 PLIP interactions: 14 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:T.38, D:Y.41, D:F.42, D:F.42, D:V.67, D:L.88, D:L.88, D:L.96, D:V.98, D:F.103, D:F.106, D:L.141 pi-Stacking: D:H.63 Metal complexes: D:H.92, H2O.19

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: K.100, I.101, H.104 Chain B: D.108, Q.131 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Water bridges: A:K.100, A:K.100, A:H.104, B:E.104, B:D.108, B:D.108, B:Q.131 Hydrogen bonds: B:Q.131 GOL.6: 5 residues within 4Å: Chain C: K.100, I.101, H.104 Chain D: D.108, Q.131 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Water bridges: C:K.100, C:K.100, C:H.104, D:E.104, D:D.108, D:D.108, D:Q.131 Hydrogen bonds: D:Q.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ariaeenejad, S. et al., Novel X-ray sequences and crystal structures of Persian and Starry sturgeon methemoglobins: Highlighting the role of heme pocket waters in causing autoxidation. Biochim Biophys Acta Proteins Proteom (2019)

Release Date

2019-04-10

Peptides

Alpha chain: AC
Beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Alpha chain

Beta chain