SMTL ID : 3anz.2 (3 other biounits)

Crystal Structure of alpha-hemolysin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-heptamer

Ligands

14 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 7 residues within 4Å: Chain A: N.177, Q.178, W.180, Q.195, M.198, K.199, R.201 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.201 Hydrogen bonds: A:R.201 MPD.2: 6 residues within 4Å: Chain A: N.179, W.180, G.181 Chain F: S.115, L.117 Chain G: H.145 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain G, 2 interactions with chain A Hydrophobic interactions: F:L.117, G:H.145, A:W.180 Hydrogen bonds: A:G.181 MPD.5: 7 residues within 4Å: Chain B: N.177, Q.178, W.180, Q.195, M.198, K.199, R.201 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.180, B:R.201 Hydrogen bonds: B:Q.195 MPD.6: 7 residues within 4Å: Chain A: H.145, L.147 Chain B: N.179, W.180, G.181 Chain G: S.115, L.117 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.180, A:L.147 Hydrogen bonds: B:N.179 MPD.7: 9 residues within 4Å: Chain C: N.177, Q.178, W.180, Y.183, Q.195, M.198, K.199, T.200, R.201 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Q.178, C:W.180, C:R.201 Hydrogen bonds: C:M.198 MPD.8: 7 residues within 4Å: Chain A: S.115, L.117 Chain B: H.145, L.147 Chain C: N.179, W.180, G.181 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:W.180, B:H.145, A:L.117 Hydrogen bonds: C:G.181, C:G.181 MPD.10: 7 residues within 4Å: Chain D: N.177, W.180, Q.195, M.198, K.199, T.200, R.201 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.180, D:R.201 Hydrogen bonds: D:Q.195 MPD.11: 6 residues within 4Å: Chain B: S.115, T.116, I.143 Chain D: N.179, W.180, G.181 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.180 Hydrogen bonds: D:G.181 MPD.14: 7 residues within 4Å: Chain E: N.177, Q.178, W.180, Q.195, M.198, K.199, R.201 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:W.180, E:Q.195, E:R.201 Hydrogen bonds: E:M.198, E:R.201 MPD.15: 6 residues within 4Å: Chain C: S.115, L.117 Chain D: Y.113, H.145, L.147 Chain E: G.181 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: C:L.117, D:Y.113 Hydrogen bonds: C:S.115, E:G.181 MPD.17: 8 residues within 4Å: Chain F: N.177, Q.178, W.180, Q.195, M.198, K.199, T.200, R.201 No protein-ligand interaction detected (PLIP) MPD.18: 6 residues within 4Å: Chain D: S.115 Chain E: H.145, L.147 Chain F: N.179, W.180, G.181 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:W.180, E:L.147 Hydrogen bonds: F:G.181 MPD.20: 8 residues within 4Å: Chain G: N.177, Q.178, W.180, Q.195, M.198, K.199, T.200, R.201 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:R.201 Hydrogen bonds: G:M.198 MPD.21: 6 residues within 4Å: Chain E: S.115 Chain F: H.145, L.147 Chain G: N.179, W.180, G.181 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: F:L.147, G:W.180 Hydrogen bonds: G:G.181

7 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 1 residues within 4Å: Chain A: A.139 No protein-ligand interaction detected (PLIP) ACY.4: 2 residues within 4Å: Chain A: N.122 Chain B: A.139 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.139 ACY.9: 2 residues within 4Å: Chain C: A.139, N.140 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.139 ACY.12: 2 residues within 4Å: Chain D: A.139, N.140 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.139 ACY.13: 2 residues within 4Å: Chain D: F.121 Chain E: V.141 No protein-ligand interaction detected (PLIP) ACY.16: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:A.139 ACY.19: 1 residues within 4Å: Chain G: A.139 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:A.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, Y. et al., 2-Methyl-2,4-pentanediol induces spontaneous assembly of staphylococcal alpha-hemolysin into heptameric pore structure. Protein Sci. (2011)

Release Date

2011-06-22

Peptides

Alpha-hemolysin: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
J

D
K

E
L

F
M

G
N

Membrane

We predict this structure to be a membrane protein.
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Alpha-hemolysin

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