SMTL ID : 1yew.5 (5 other biounits)

Crystal structure of particulate methane monooxygenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-6-6-6-mer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.16, H.40, L.358, Q.372 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.16, A:H.40 CU.6: 4 residues within 4Å: Chain D: H.16, H.40, L.358, Q.372 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.16, D:H.40 CU.12: 4 residues within 4Å: Chain G: H.16, H.40, L.358, Q.372 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:H.16, G:H.40 CU.15: 4 residues within 4Å: Chain J: H.16, H.40, L.358, Q.372 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:H.16, J:H.40 CU.20: 4 residues within 4Å: Chain M: H.16, H.40, L.358, Q.372 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:H.16, M:H.40 CU.26: 4 residues within 4Å: Chain P: H.16, H.40, L.358, Q.372 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:H.16, P:H.40

16 x ZN: ZINC ION(Non-covalent)

ZN.2: 1 residues within 4Å: Chain A: E.25 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.25, A:E.25 ZN.4: 4 residues within 4Å: Chain B: E.195 Chain C: D.156, H.160, H.173 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Metal complexes: C:D.156, C:D.156, C:H.160, C:H.173, B:E.195 ZN.5: 3 residues within 4Å: Chain B: H.11 Chain C: H.231, W.234 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.231 ZN.7: 4 residues within 4Å: Chain D: D.294, D.296, D.312 Ligands: ZN.9 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.294, D:D.296 ZN.8: 4 residues within 4Å: Chain D: H.275 Chain M: T.273, H.275 Ligands: ZN.22 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.275 ZN.9: 2 residues within 4Å: Chain D: S.315 Ligands: ZN.7 No protein-ligand interaction detected (PLIP) ZN.11: 4 residues within 4Å: Chain E: E.195 Chain F: D.156, H.160, H.173 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.156, F:D.156, F:H.160, F:H.173 ZN.14: 4 residues within 4Å: Chain H: E.195 Chain I: D.156, H.160, H.173 5 PLIP interactions: 1 interactions with chain H, 4 interactions with chain I Metal complexes: H:E.195, I:D.156, I:D.156, I:H.160, I:H.173 ZN.16: 1 residues within 4Å: Chain J: E.25 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:E.25, J:E.25 ZN.18: 4 residues within 4Å: Chain K: E.195 Chain L: D.156, H.160, H.173 5 PLIP interactions: 1 interactions with chain K, 4 interactions with chain L Metal complexes: K:E.195, L:D.156, L:D.156, L:H.160, L:H.173 ZN.19: 3 residues within 4Å: Chain K: H.11 Chain L: H.231, W.234 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:H.231 ZN.21: 4 residues within 4Å: Chain M: D.294, D.296, D.312 Ligands: ZN.23 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.294, M:D.296 ZN.22: 4 residues within 4Å: Chain D: T.273, H.275 Chain M: H.275 Ligands: ZN.8 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:H.275 ZN.23: 2 residues within 4Å: Chain M: S.315 Ligands: ZN.21 No protein-ligand interaction detected (PLIP) ZN.25: 4 residues within 4Å: Chain N: E.195 Chain O: D.156, H.160, H.173 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:D.156, O:D.156, O:H.160, O:H.173 ZN.28: 4 residues within 4Å: Chain Q: E.195 Chain R: D.156, H.160, H.173 5 PLIP interactions: 4 interactions with chain R, 1 interactions with chain Q Metal complexes: R:D.156, R:D.156, R:H.160, R:H.173, Q:E.195

6 x CUA: DINUCLEAR COPPER ION(Covalent)

CUA.3: 4 residues within 4Å: Chain A: H.1, H.105, H.107, G.122 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.1, A:H.105, A:H.107, A:H.107 CUA.10: 4 residues within 4Å: Chain D: H.1, H.105, H.107, G.122 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.1, D:H.105, D:H.107, D:H.107 CUA.13: 4 residues within 4Å: Chain G: H.1, H.105, H.107, G.122 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.1, G:H.105, G:H.107, G:H.107 CUA.17: 4 residues within 4Å: Chain J: H.1, H.105, H.107, G.122 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:H.1, J:H.105, J:H.107, J:H.107 CUA.24: 4 residues within 4Å: Chain M: H.1, H.105, H.107, G.122 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:H.1, M:H.105, M:H.107, M:H.107 CUA.27: 4 residues within 4Å: Chain P: H.1, H.105, H.107, G.122 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:H.1, P:H.105, P:H.107, P:H.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lieberman, R.L. et al., Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane. Nature (2005)

Release Date

2005-02-08

Peptides

particulate methane monooxygenase, B subunit: ADGJMP
particulate methane monooxygenase, A subunit: BEHKNQ
particulate methane monooxygenase subunit C2: CFILOR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

G
I

J
A

M
E

P
I

B
B

E
F

H
J

K
B

N
F

Q
J

C
C

F
G

I
K

L
C

O
G

R
K

Membrane

We predict this structure to be a membrane protein.
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particulate methane monooxygenase, B subunit

particulate methane monooxygenase, A subunit

particulate methane monooxygenase subunit C2

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