SMTL ID : 9nh3.1

Helicobacter pylori strain SS1 KatA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 34 residues within 4Å: Chain A: R.53, V.54, V.55, H.56, R.93, S.95, G.112, F.113, A.114, V.127, G.128, N.129, F.134, I.136, A.139, F.142, F.196, G.197, S.198, H.199, V.280, A.314, F.315, M.331, G.334, R.335, S.338, Y.339, T.342, H.343, R.346 Chain C: L.42, F.45, D.46 31 PLIP interactions: 30 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:V.54, A:V.55, A:H.56, A:A.114, A:V.127, A:N.129, A:A.139, A:F.142, A:F.142, A:F.142, A:F.142, A:R.335, A:Y.339, A:Y.339, A:T.342, C:L.42 Water bridges: A:A.114, A:T.342, A:T.342, A:H.343, A:R.346 Salt bridges: A:R.53, A:R.53, A:R.93, A:H.343, A:R.346 pi-Stacking: A:H.56, A:F.134, A:F.142 pi-Cation interactions: A:R.335 Metal complexes: A:Y.339 HEM.6: 34 residues within 4Å: Chain B: R.53, V.54, V.55, H.56, R.93, S.95, G.112, F.113, A.114, V.127, G.128, N.129, F.134, I.136, A.139, F.142, F.196, G.197, S.198, H.199, V.280, A.314, F.315, M.331, G.334, R.335, S.338, Y.339, T.342, H.343, R.346 Chain D: L.42, F.45, D.46 29 PLIP interactions: 28 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: B:V.54, B:V.55, B:H.56, B:V.127, B:N.129, B:A.139, B:F.142, B:F.142, B:F.142, B:F.142, B:R.335, B:Y.339, B:Y.339, B:T.342, D:L.42 Water bridges: B:R.93, B:T.342, B:H.343, B:R.346 Salt bridges: B:R.53, B:R.53, B:R.93, B:H.343, B:R.346 pi-Stacking: B:H.56, B:F.134, B:F.142 pi-Cation interactions: B:R.335 Metal complexes: B:Y.339 HEM.12: 34 residues within 4Å: Chain A: L.42, F.45, D.46 Chain C: R.53, V.54, V.55, H.56, R.93, S.95, G.112, F.113, A.114, V.127, G.128, N.129, F.134, I.136, A.139, F.142, F.196, G.197, S.198, H.199, V.280, A.314, F.315, M.331, G.334, R.335, S.338, Y.339, T.342, H.343, R.346 31 PLIP interactions: 30 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:V.54, C:V.55, C:H.56, C:A.114, C:V.127, C:N.129, C:A.139, C:F.142, C:F.142, C:F.142, C:F.142, C:R.335, C:Y.339, C:Y.339, C:T.342, A:L.42 Water bridges: C:A.114, C:T.342, C:T.342, C:H.343, C:R.346 Salt bridges: C:R.53, C:R.53, C:R.93, C:H.343, C:R.346 pi-Stacking: C:H.56, C:F.134, C:F.142 pi-Cation interactions: C:R.335 Metal complexes: C:Y.339 HEM.17: 34 residues within 4Å: Chain B: L.42, F.45, D.46 Chain D: R.53, V.54, V.55, H.56, R.93, S.95, G.112, F.113, A.114, V.127, G.128, N.129, F.134, I.136, A.139, F.142, F.196, G.197, S.198, H.199, V.280, A.314, F.315, M.331, G.334, R.335, S.338, Y.339, T.342, H.343, R.346 29 PLIP interactions: 28 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: D:V.54, D:V.55, D:H.56, D:V.127, D:N.129, D:A.139, D:F.142, D:F.142, D:F.142, D:F.142, D:R.335, D:Y.339, D:Y.339, D:T.342, B:L.42 Water bridges: D:R.93, D:T.342, D:H.343, D:R.346 Salt bridges: D:R.53, D:R.53, D:R.93, D:H.343, D:R.346 pi-Stacking: D:H.56, D:F.134, D:F.142 pi-Cation interactions: D:R.335 Metal complexes: D:Y.339

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 13 residues within 4Å: Chain A: K.77, I.204, V.320, V.321, P.322, G.323, I.324, G.325, A.397, R.398, D.399, P.400 Chain D: W.17 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.323, A:I.324, A:A.397, D:W.17 Water bridges: A:K.77 GOL.8: 14 residues within 4Å: Chain B: K.77, I.204, V.320, V.321, P.322, G.323, I.324, G.325, Y.326, A.397, R.398, D.399, P.400 Chain C: W.17 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.323, B:I.324 Water bridges: B:K.77, B:A.397, B:D.399, C:W.17, C:W.17, C:W.17, C:W.17 GOL.13: 13 residues within 4Å: Chain B: W.17 Chain C: K.77, I.204, V.320, V.321, P.322, G.323, I.324, G.325, A.397, R.398, D.399, P.400 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.323, C:I.324, C:A.397, B:W.17 Water bridges: C:K.77 GOL.19: 14 residues within 4Å: Chain A: W.17 Chain D: K.77, I.204, V.320, V.321, P.322, G.323, I.324, G.325, Y.326, A.397, R.398, D.399, P.400 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:G.323, D:I.324 Water bridges: D:K.77, D:A.397, D:D.399, A:W.17, A:W.17, A:W.17, A:W.17

12 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: P.266, D.269, Y.289 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.269 NA.4: 2 residues within 4Å: Chain A: R.244, D.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.248 NA.5: 3 residues within 4Å: Chain A: E.304 Chain C: Q.154 Chain D: S.379 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.154, D:S.379 Water bridges: D:S.379 NA.9: 6 residues within 4Å: Chain B: S.182, D.183, R.184, Y.432, L.436, E.440 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.183, B:R.184, B:R.184, B:E.440 Water bridges: B:R.184 NA.10: 4 residues within 4Å: Chain B: E.121 Chain C: T.9, G.13, P.15 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:E.121 Hydrogen bonds: C:G.13 NA.11: 3 residues within 4Å: Chain B: D.152, N.159, M.162 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.159 NA.14: 3 residues within 4Å: Chain C: P.266, D.269, Y.289 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.269 NA.15: 2 residues within 4Å: Chain C: R.244, D.248 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.248 NA.16: 3 residues within 4Å: Chain A: Q.154 Chain B: S.379 Chain C: E.304 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.154, A:Q.154 Water bridges: B:S.379 NA.20: 6 residues within 4Å: Chain D: S.182, D.183, R.184, Y.432, L.436, E.440 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.182, D:D.183, D:R.184, D:R.184 Water bridges: D:R.184 NA.21: 4 residues within 4Å: Chain A: T.9, G.13, P.15 Chain D: E.121 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.13 NA.22: 3 residues within 4Å: Chain D: D.152, N.159, M.162 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.152, D:D.152

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: Y.345 Chain B: Y.345 Chain C: R.47 Chain D: R.47 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain A: R.47 Chain B: R.47 Chain C: Y.345 Chain D: Y.345 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baylink, A., AlphaFold 3 accurately models natural variants of Helicobacter pylori catalase KatA. Biorxiv (2025)

Release Date

2025-07-23

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Catalase