SMTL ID : 3dzm.4 (4 other biounits)

Crystal structure of a major outer membrane protein from Thermus thermophilus HB27

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.52, L.54, D.56, K.70, E.77 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.52, A:L.54, A:D.56, A:E.77 CA.4: 5 residues within 4Å: Chain B: D.52, L.54, D.56, K.70, E.77 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:L.54, B:D.56, B:E.77, B:E.77 CA.7: 4 residues within 4Å: Chain C: D.52, L.54, D.56, E.77 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.52, C:L.54, C:D.56, C:E.77 CA.10: 5 residues within 4Å: Chain D: D.52, L.54, D.56, K.70, E.77 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.52, D:L.54, D:D.56, D:E.77 CA.13: 5 residues within 4Å: Chain E: D.52, L.54, D.56, K.70, E.77 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:L.54, E:D.56, E:E.77, E:E.77 CA.16: 4 residues within 4Å: Chain F: D.52, L.54, D.56, E.77 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.52, F:L.54, F:D.56, F:E.77

12 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)

C8E.2: 9 residues within 4Å: Chain A: G.21, S.51, N.81, F.112, T.198, Q.199, P.200, E.201, W.202 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.202 Hydrogen bonds: A:S.51, A:N.81, A:N.81, A:E.201, A:W.202 C8E.3: 6 residues within 4Å: Chain A: Y.161, Q.164, N.194, V.197, Q.199, E.201 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.161, A:Y.161 Hydrogen bonds: A:Q.164, A:N.194, A:V.197, A:Q.199, A:Q.199 C8E.5: 11 residues within 4Å: Chain B: G.21, S.51, N.81, Y.161, T.198, Q.199, P.200, E.201, W.202, V.203 Ligands: C8E.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.51, B:N.81, B:N.81, B:E.201, B:W.202 C8E.6: 9 residues within 4Å: Chain B: Y.161, F.163, Q.164, N.194, V.197, T.198, Q.199, E.201 Ligands: C8E.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.163, B:Q.164 Hydrogen bonds: B:Y.161, B:Q.164, B:Q.164, B:N.194, B:Q.199, B:Q.199, B:Q.199, B:E.201 C8E.8: 9 residues within 4Å: Chain C: Y.161, Y.162, F.163, Q.164, N.194, V.197, T.198, Q.199, E.201 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.163, C:F.163 Hydrogen bonds: C:Q.164, C:N.194, C:Q.199, C:Q.199, C:Q.199 C8E.9: 13 residues within 4Å: Chain C: G.21, S.51, D.52, N.81, F.112, T.198, Q.199, P.200, E.201, W.202, V.203 Chain F: P.98, Y.145 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain C Hydrophobic interactions: F:P.98 Hydrogen bonds: F:Y.145, C:S.51, C:E.201, C:W.202 C8E.11: 9 residues within 4Å: Chain D: G.21, S.51, N.81, F.112, T.198, Q.199, P.200, E.201, W.202 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.202 Hydrogen bonds: D:S.51, D:N.81, D:N.81, D:E.201, D:W.202 C8E.12: 6 residues within 4Å: Chain D: Y.161, Q.164, N.194, V.197, Q.199, E.201 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.161, D:Y.161 Hydrogen bonds: D:Y.161, D:Q.164, D:N.194, D:V.197, D:Q.199, D:Q.199 C8E.14: 11 residues within 4Å: Chain E: G.21, S.51, N.81, Y.161, T.198, Q.199, P.200, E.201, W.202, V.203 Ligands: C8E.15 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:S.51, E:N.81, E:N.81, E:E.201, E:W.202 C8E.15: 9 residues within 4Å: Chain E: Y.161, F.163, Q.164, N.194, V.197, T.198, Q.199, E.201 Ligands: C8E.14 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.163, E:Q.164 Hydrogen bonds: E:Q.164, E:Q.164, E:N.194, E:Q.199, E:Q.199, E:Q.199 C8E.17: 9 residues within 4Å: Chain F: Y.161, Y.162, F.163, Q.164, N.194, V.197, T.198, Q.199, E.201 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:F.163, F:F.163 Hydrogen bonds: F:Y.161, F:Q.164, F:N.194, F:Q.199, F:Q.199, F:Q.199, F:E.201 C8E.18: 13 residues within 4Å: Chain C: P.98, Y.145 Chain F: G.21, S.51, D.52, N.81, F.112, T.198, Q.199, P.200, E.201, W.202, V.203 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain F Hydrophobic interactions: C:P.98 Hydrogen bonds: F:S.51, F:E.201, F:E.201, F:W.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brosig, A. et al., Crystal structure of a major outer membrane protein from Thermus thermophilus HB27. J.Mol.Biol. (2009)

Release Date

2008-12-23

Peptides

Hypothetical conserved protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Hypothetical conserved protein

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