SMTL ID : 2pnk.5 (5 other biounits)

CRYSTAL STRUCTURE OF AN URONATE ISOMERASE (BH0493) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: E.333 Chain B: E.333 Chain C: E.333 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.333 NA.14: 2 residues within 4Å: Chain E: E.333 Chain F: E.333 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:E.333, D:E.333, D:E.333

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

CL.2: 6 residues within 4Å: Chain A: K.279, E.305 Chain B: K.279, E.305 Chain C: K.279, E.305 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain D: K.279, E.305 Chain E: K.279, E.305 Chain F: K.279, E.305 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain F: Y.179, E.180, N.236 Ligand excluded by PLIP

7 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 8 residues within 4Å: Chain A: R.315, K.316 Chain B: H.50, Y.51, A.54, A.273, W.327, F.328 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.327, A:R.315, A:K.316 FMT.9: 7 residues within 4Å: Chain B: R.315, K.316 Chain C: H.50, A.54, A.273, W.327, F.328 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.315, B:K.316, C:W.327 FMT.12: 6 residues within 4Å: Chain A: H.50, A.54, W.327, F.328 Chain C: R.315, K.316 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.315, C:R.315, C:K.316 FMT.17: 6 residues within 4Å: Chain D: R.315, K.316 Chain E: H.50, A.54, W.327, F.328 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:R.315, D:R.315, D:K.316, E:H.50 FMT.18: 7 residues within 4Å: Chain D: H.27, T.144, R.171, D.173, V.223, S.224, M.259 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.224 Water bridges: D:S.224, D:S.224 FMT.22: 8 residues within 4Å: Chain E: R.315, K.316 Chain F: H.50, Y.51, A.54, A.273, W.327, F.328 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:H.50, F:W.327, E:R.315, E:K.316 FMT.31: 6 residues within 4Å: Chain D: H.50, A.54, W.327, F.328 Chain F: R.315, K.316 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:H.50, F:R.315, F:R.315, F:K.316

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: N.177, E.178, Y.179, E.180, Q.181, N.236 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.177, A:Y.179, A:E.180, A:Q.181, A:N.236 Water bridges: A:N.236, A:N.236, A:R.237 GOL.5: 7 residues within 4Å: Chain A: H.29, H.50, Y.51, W.326, W.327, D.356, R.358 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.51, A:D.356, A:R.358, A:R.358 Water bridges: A:Y.49, A:D.275, A:D.275, A:W.327, A:N.330 GOL.6: 3 residues within 4Å: Chain A: D.211, W.212, R.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.211 Water bridges: A:D.211 GOL.7: 6 residues within 4Å: Chain A: F.231, P.232, D.283, E.286, H.287, R.290 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.231, A:E.286, A:H.287, A:R.290 Water bridges: A:F.231 GOL.10: 6 residues within 4Å: Chain B: H.50, Y.51, W.326, W.327, D.356, R.358 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.51, B:R.358, B:R.358 Water bridges: B:Y.49, B:D.275, B:D.356, B:D.356 GOL.19: 6 residues within 4Å: Chain D: H.50, Y.51, W.326, W.327, D.356, R.358 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.356, D:R.358, D:R.358 Water bridges: D:Y.51, D:N.330 GOL.20: 3 residues within 4Å: Chain D: P.227, K.279, A.280 1 PLIP interactions: 1 interactions with chain D Water bridges: D:K.279 GOL.23: 6 residues within 4Å: Chain E: H.50, Y.51, W.326, W.327, D.356, R.358 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:R.358 Water bridges: E:Y.49, E:Y.51, E:Y.51, E:R.358 GOL.24: 1 residues within 4Å: Chain E: R.399 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:R.399 Water bridges: E:E.395, E:E.396, F:I.85, F:K.86 GOL.25: 1 residues within 4Å: Chain E: E.158 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.158 GOL.26: 3 residues within 4Å: Chain D: R.340 Chain E: P.332, E.333 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:P.332 Water bridges: E:N.336, D:R.340, D:R.340, D:R.340 GOL.32: 6 residues within 4Å: Chain F: H.50, Y.51, W.326, W.327, D.356, R.358 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:D.356, F:R.358 Water bridges: F:Y.49, F:Y.51, F:N.330, F:R.358 GOL.33: 3 residues within 4Å: Chain F: K.279, A.280, S.281 4 PLIP interactions: 4 interactions with chain F Water bridges: F:K.279, F:K.279, F:A.280, F:N.306

2 x UNL: UNKNOWN LIGAND(Non-functional Binders)

UNL.8: 7 residues within 4Å: Chain B: N.177, E.178, Y.179, E.180, S.235, N.236, R.237 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:N.177, B:N.177, B:N.177, B:E.180, B:S.235, B:N.236, B:N.236, B:R.237 Water bridges: B:Y.179, B:Y.179, B:E.180, B:E.180, B:Q.181, B:E.233, B:S.235, B:R.237, B:R.237 UNL.16: 8 residues within 4Å: Chain D: N.177, E.178, Y.179, E.180, Q.181, S.235, N.236, R.237 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:L.176, D:E.178, D:Y.179, D:E.180, D:Q.181, D:N.236, D:N.236, D:R.237 Water bridges: D:S.235, D:R.237, D:R.237

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.11: 7 residues within 4Å: Chain C: H.29, H.50, Y.51, W.326, W.327, D.356, R.358 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.51, C:W.327 Water bridges: C:Y.49 Salt bridges: C:H.29, C:H.50, C:R.358 PO4.21: 3 residues within 4Å: Chain E: E.158, G.159, K.160 No protein-ligand interaction detected (PLIP)

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

MPD.13: 4 residues within 4Å: Chain C: P.227, T.228, K.279, S.281 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.228 MPD.27: 4 residues within 4Å: Chain E: L.157, Y.191, D.211, W.212 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.157, E:Y.191, E:W.212 Water bridges: E:D.211 MPD.28: 5 residues within 4Å: Chain E: P.227, T.228, K.279, A.280, S.281 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:K.279 Hydrogen bonds: E:P.227 MPD.34: 5 residues within 4Å: Chain F: L.157, Y.191, D.211, W.212, R.215 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:D.211, F:W.212, F:W.212, F:R.215 Hydrogen bonds: F:Y.191, F:Y.191

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.30: 8 residues within 4Å: Chain F: H.27, H.29, T.144, R.171, D.173, A.222, S.224, M.259 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:T.144, F:R.171, F:A.222 Hydrogen bonds: F:H.27, F:S.224 Salt bridges: F:R.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of uncharacterized protein (NP_241359.1) from Bacillus halodurans at 2.00 A resolution. To be published

Release Date

2007-05-08

Peptides

BH0493 protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
J

E
K

F
L

BH0493 protein

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