SMTL ID : 4phz.1

Crystal structure of particulate methane monooxygenase from Methylocystis sp. ATCC 49242 (Rockwell)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

6 x CU: COPPER (II) ION(Non-covalent)

CU.1: 3 residues within 4Å: Chain C: D.129, H.133, H.146 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.129, C:H.133, C:H.146 CU.3: 3 residues within 4Å: Chain E: H.29, H.133, H.135 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.29, E:H.133, E:H.135 CU.4: 3 residues within 4Å: Chain G: H.29, H.133, H.135 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:H.133, G:H.135 CU.5: 3 residues within 4Å: Chain H: H.29, H.133, H.135 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.133, H:H.135, H2O.3 CU.6: 3 residues within 4Å: Chain K: D.129, H.133, H.146 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:D.129, K:H.133, K:H.146 CU.8: 3 residues within 4Å: Chain L: D.129, H.133, H.146 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:D.129, L:H.133, L:H.146

4 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Covalent)(Non-covalent)

PGT.2: 25 residues within 4Å: Chain C: G.23, M.24, G.27, L.31, S.76, L.80, A.81, G.82, Y.83, L.84, W.85, R.102, V.106, Q.109, W.110, V.113, V.159, V.162, G.163, F.166, Y.167, R.171 Chain D: X.21, X.23, X.24 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:L.31, C:A.81, C:L.84, C:L.84, C:L.84, C:W.85, C:W.85, C:Q.109, C:W.110, C:W.110, C:W.110, C:V.113, C:V.159, C:V.162, C:F.166, C:F.166, C:F.166, C:Y.167, C:Y.167 Water bridges: C:Y.83, C:R.171 Salt bridges: C:R.102, C:R.171 PGT.7: 21 residues within 4Å: Chain A: X.8, X.11 Chain K: G.23, M.24, G.27, L.30, L.31, F.34, S.76, G.79, L.80, Y.83, L.84, T.87, R.102, V.106, Q.109, W.110, V.113, Y.167, R.171 16 PLIP interactions: 16 interactions with chain K Hydrophobic interactions: K:L.31, K:F.34, K:L.80, K:Y.83, K:Y.83, K:Y.83, K:L.84, K:V.106, K:W.110, K:V.113, K:Y.167 Hydrogen bonds: K:Y.167, K:Y.167, K:R.171 Salt bridges: K:R.102, K:R.171 PGT.9: 23 residues within 4Å: Chain B: X.7, X.8, X.11, X.12, X.13, X.16, X.19 Chain L: G.23, G.27, L.30, L.31, F.34, L.80, Y.83, L.84, R.102, V.106, Q.109, W.110, V.113, I.160, Y.167, R.171 9 PLIP interactions: 9 interactions with chain L Hydrophobic interactions: L:L.31, L:F.34, L:L.80, L:Y.83, L:Q.109, L:V.113, L:I.160 Salt bridges: L:R.102, L:R.171 PGT.10: 16 residues within 4Å: Chain I: I.252 Chain L: E.73, L.74, G.77, L.78, A.81, G.82, W.85, F.165, F.166, K.169, A.176, G.178, Y.179, I.188, F.191 15 PLIP interactions: 1 interactions with chain I, 14 interactions with chain L Hydrophobic interactions: I:I.252, L:A.81, L:W.85, L:F.165, L:F.166, L:F.166, L:I.188, L:I.188, L:F.191, L:F.191, L:F.191 Hydrogen bonds: L:K.169, L:Y.179 Water bridges: L:K.169, L:A.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sirajuddin, S. et al., Effects of zinc on particulate methane monooxygenase activity and structure. J.Biol.Chem. (2014)

Release Date

2014-06-25

Peptides

unknown peptide: ABD
Particulate methane monooxygenase subunit C: CKL
Particulate methane monooxygenase subunit B: EGH
Particulate methane monooxygenase subunit A: FIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
H

D
N

C
K

K
C

L
G

E
A

G
E

H
I

F
B

I
F

J
J

Membrane

We predict this structure to be a membrane protein.
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unknown peptide

Particulate methane monooxygenase subunit C

Particulate methane monooxygenase subunit B

Particulate methane monooxygenase subunit A

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